Methods and compositions for inhibition of hao1 (hydroxyacid oxidase 1 (glycolate oxidase)) gene expression

ABSTRACT

The invention relates methods of using RNAi agents to inhibit expression of HAO1 and methods of treating subjects having primary hyperoxaluria, e.g., PH1.

RELATED APPLICATIONS

This application is a 35 § U.S.C. 111(a) continuation application which claims the benefit of priority to PCT/US2021/061315, filed on Dec. 1, 2021, which, in turn, claims the benefit of priority to U.S. Provisional Application No. 63/120,150, filed on Dec. 1, 2020, and U.S. Provisional Application No. 63/182,608, filed on Apr. 30, 2021. The entire contents of each of the foregoing applications are incorporated herein by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in XML file format and is hereby incorporated by reference in its entirety. Said XML copy, created on May 15, 2023, is named 121301-19903_SL.xml and is 66,035 bytes in size.

BACKGROUND OF THE INVENTION

Oxalate (C2O42-) is the salt-forming ion of oxalic acid (C2H2O4) that is widely distributed in both plants and animals. It is a component of human diet and is ubiquitously found in plants and plant-derived foods. Oxalate can also be synthesized endogenously via the metabolic pathway that occurs primarily in the liver. Glyoxylate is an immediate precursor to oxalate and is derived from the oxidation of glycolate by the enzyme glycolate oxidase (GO), also known, and referred to herein, as hydroxyacid oxidase (HAO1), or by catabolism of hydroxyproline, a component of collagen. Transamination of glyoxylate with alanine by the enzyme alanine/glyoxylate aminotransferase (AGT) results in the formation of pyruvate and glycine. Excess glyoxylate will be converted to oxalate by glycolate oxidase or lactate dehydrogenase.

Primary hyperoxaluria (PH) is a group of inherited disorders of the liver characterized by increased urinary excretion of oxalate, an end-product of metabolism. There are 3 types of PH: type 1 (PH1), type 2 (PH2), and type 3 (PH3). PH1 is the most common and the most severe form, accounting for 70% to 80% of all cases. PH1 is an ultra-rare, inherited disease in which excessive amounts of oxalate are produced by the liver. PH1 affects approximately 4 individuals per million in the United States and Europe, with an estimated 1,300 to 2,100 diagnosed cases. In some regions, such as the Middle East and North Africa, the genetic prevalence of PH1 is higher.

Primary Hyperoxaluria Type 1 (PH1) is an autosomal recessive disorder of glyoxylate metabolism characterized by excessive oxalate production by the liver and consequent hyperoxaluria. Hepatic glyoxylate detoxification is impaired due to mutation in the alanine-glyoxylate aminotransferase (AGXT) gene. Loss of AGT function to convert the intermediate metabolite glyoxylate to glycine causes accumulation and reduction of glyoxylate to glycolate which is oxidized to oxalate by the enzyme glycolate oxidase (GO), also known as hydroxyacid oxidase (HAO1) and ultimately transported to the kidneys for excretion. Oxalate, in the form of its calcium salt, is excreted almost entirely by the kidney. Due to its insolubility, calcium oxalate can crystallize readily in the urinary tract. In PH1, excess urinary oxalate results in formation and deposition of calcium oxalate crystals in the kidneys and urinary tract leading to recurrent nephrolithiasis and/or nephrocalcinosis, which can lead to pain, infections, progressive kidney disease and failure, along with reduced quality of life (Cochat (2013) N Engl J Med. 369(7):649-58). Renal damage is caused by a combination of tubular toxicity from oxalate, nephrocalcinosis and renal obstruction by stones.

As renal function declines, elimination of oxalate is further reduced, such that calcium oxalate accumulates in bone, vasculature, skin, retina, heart, and nervous system, resulting in severe end-organ damage (Cochat, supra). This devastating condition, systemic oxalosis, arises when the estimated glomerular filtration rate (eGFR) has declined to below 30 to 45 mL/min/1.73 m². Without treatment, the disease progresses inexorably, and death from end-stage renal disease (ESRD) and/or complications of oxalosis is inevitable (Cochat supra; Harambat (2010) Kidney Int. 77(5):443-9; van der Hoeven (2012) Nephrol Dial Transplant. 18(2):273-9).

Until the recent approval of lumasiran, there were no approved therapies for the treatment of PH and the standard of care was burdensome to patients and their families. Disease management was based on supportive measures, including high fluid intake and crystallization inhibitors to increase urinary oxalate solubility, and treatment of disease complications such as urinary tract stones and infections in those that do not yet have ESRD. Pyridoxine can normalize hepatic oxalate production (and consequently urinary oxalate) in a small subset (˜5%) of patients. Dietary modification plays a minor role in treatment since endogenous oxalate production far exceeds dietary intake in patients with PH. Patients progressing to, or presenting with ESRD, require intense dialysis replacement therapy. Dialysis is not viewed as an effective therapy for PH1, but rather serves as a step in the clinical course toward a liver-kidney transplant or as an alternative to no therapy at all. Dialysis is often inadequate to effectively offload accumulating oxalate, and systemic oxalosis with end organ damage may develop despite this burdensome treatment. Dialysis regimens for PH1 are typically more frequent than conventional dialysis, predisposing to increased risk of complications. Combined liver-kidney transplantation offers potentially curative therapy, but is limited due to restricted availability, complications associated with the procedure, ethical considerations in resource-poor settings, and intense use of health care resources.

Accordingly, there is a need in the art for effective methods for treating primary hyperoxaluria.

SUMMARY OF THE INVENTION

The present invention provides methods for inhibiting HAO1 expression. The present invention also provides methods for treating a subject having an HAO1 associated disorders, e.g., primary hyperoxaluria (PH), e.g., PH1, as well as methods for reducing plasma oxalate, reducing medullary nephrocalcinosis, and reducing systemic oxalosis in a subject having an HAO1 associated disorders, e.g., primary hyperoxaluria (PH), e.g., PH1. The methods include administering a double stranded RNAi agent, e.g., a double-stranded iRNA agent targeting HAO1, and compositions comprising such double stranded RNAi agents, in a dosing regimen which includes a loading phase and a maintenance phase.

Accordingly, in one aspect, the present invention provides a method for inhibiting expression of hydroxyacid oxidase (HAO1) in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13) (SEQ ID NO:13), thereby inhibiting the expression of HAO1 in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for inhibiting expression of hydroxyacid oxidase (HAO1) in a human subject having primary hyperoxaluria. The method includes administering to the subject a therapeutically effective amount of a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby inhibiting the expression of HAO1 in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

In another aspect, the present invention provides a method for inhibiting expression of hydroxyacid oxidase (HAO1) in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby inhibiting the expression of HAO1 in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

Inhibiting HAO1 expression in the subject may reduce plasma oxalate levels in the subject; reduce medullary nephrocalcinosis in the subject; reduce systemic oxalosis, e.g., renal oxalosis, cardiac oxalosis, vascular oxalosis, skeletal oxalosis, dermatologic oxalosis, and/or ophthalmic oxalosis, e.g., cardiac oxalosis, in the subject; and/or reduce a hematological disorder, e.g., anemia, in the subject.

In one aspect, the present invention provides a method for treating a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby treating the human subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for treating a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby treating the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

In another aspect, the present invention provides a method for treating a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby treating the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

Treating the subject may reduce plasma oxalate levels in the subject; reduce medullary nephrocalcinosis in the subject; reduce systemic oxalosis, e.g., renal oxalosis, cardiac oxalosis, vascular oxalosis, skeletal oxalosis, dermatologic oxalosis, and/or ophthalmic oxalosis, e.g., cardiac oxalosis, in the subject; and/or reduce a hematological disorder, e.g., anemia, in the subject.

In one aspect, the present invention provides a method for reducing plasma oxalate in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing plasma oxalate in the human subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for reducing plasma oxalate in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing plasma oxalate in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

In another aspect, the present invention provides a method for reducing plasma oxalate in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing plasma oxalate in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

The plasma oxalate level may be reduced by about 35% or more following administration of the double stranded RNAi agent; and/or the plasma oxalate level is reduced to within normal range following administration of the double stranded RNAi agent.

In one aspect, the present invention provides a method for reducing medullary nephrocalcinosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing medullary nephrocalcinosis in the human subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for reducing medullary nephrocalcinosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a therapeutically effective amount of a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing medullary nephrocalcinosis in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

In another aspect, the present invention provides a method for reducing medullary nephrocalcinosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing medullary nephrocalcinosis in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

The medullary nephrocalcinosis may be reduced in one kidney or in both kidneys.

In one embodiment, the reduction in medullary nephrocalcinosis is determined by renal ultrasound.

In one aspect, the present invention provides a method for reducing systemic oxalosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing systemic oxalosis in the human subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for reducing systemic oxalosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a therapeutically effective amount of a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing systemic oxalosis in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and one month after the last dose of the loading phase the maintenance phase begins and comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject every three months.

In another aspect, the present invention provides a method for reducing systemic oxalosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a therapeutically effective amount of a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises at least 15 contiguous nucleotides from the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13), thereby reducing systemic oxalosis in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months.

In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

The systemic oxalosis may be renal oxalosis, cardiac oxalosis, vascular oxalosis, skeletal oxalosis, dermatologic oxalosis, and/or ophthalmic oxalosis.

In one embodiment, the systemic oxalosis is cardiac oxalosis.

In one embodiment, left ventricular ejection fraction (LVEF) is increased by at least about 5% following administration of the double stranded RNAi agent.

In one embodiment, global longitudinal strain (GLS) is decreased by at least about 2% following administration of the double stranded RNAi agent.

In one embodiment, early mitral inflow velocity:mitral annual early diastolic velocity (E/e′) is increased by at least about 2% following administration of the double stranded RNAi agent.

In one embodiment, reduction in systemic oxalosis is determined by an echocardiogram.

In one embodiment, the RNAi agent, or salt thereof, is administered in a pharmaceutical composition.

In one embodiment, the double stranded RNAi agent is in a salt form.

The methods of the invention may further includes administering an additional therapeutic agent to the subject.

In one embodiment, the primary hyperoxaluria is primary hyperoxaluria type I (PH1).

In one embodiment, the subject has end stage renal disease (ESRD). prior to administration of the double stranded RNAi agent.

In another embodiment, the subject does not have end stage renal disease (ESRD). prior to administration of the double stranded RNAi agent.

In one embodiment, the subject is on dialysis, e.g., hemodialysis.

In another embodiment, the subject is not on dialysis, e.g., hemodialysis.

In one embodiment, the double stranded RNAi agent is administered to the subject subcutaneously.

In one embodiment, the antisense strand comprises at least 17 contiguous nucleotides from the nucleotide sequence of 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13)′.

In another embodiment, the antisense strand comprises the nucleotide sequence of 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13)′.

In one embodiment, the sense strand comprises the nucleotide sequence 5′-GACUUUCAUCCUGGAAAUAUA-3′ (SEQ ID NO:12) and the antisense strand comprises the nucleotide sequence 5′-UAUAUUUCCAGGAUGAAAGUCCA-3′ (SEQ ID NO:13)′.

In one embodiment, the double stranded RNAi agent comprises at least one modified nucleotide.

In one embodiment, no more than five of the nucleotides of the sense strand and no more than five of the nucleotides of the antisense strand are unmodified nucleotides.

In another embodiment, all of the nucleotides of the sense strand and all of the nucleotides of the antisense strand comprise a modification.

In one embodiment, at least one of the modified nucleotides is selected from the group a deoxy-nucleotide, a 3′-terminal deoxy-thymine (dT) nucleotide, a 2′-O-methyl modified nucleotide, a 2′-fluoro modified nucleotide, a 2′-deoxy-modified nucleotide, a locked nucleotide, an unlocked nucleotide, a conformationally restricted nucleotide, a constrained ethyl nucleotide, an abasic nucleotide, a 2′-amino-modified nucleotide, a 2′-O-allyl-modified nucleotide, 2′-C-alkyl-modified nucleotide, a 2′-methoxyethyl modified nucleotide, a 2′-O-alkyl-modified nucleotide, a morpholino nucleotide, a phosphoramidate, a non-natural base comprising nucleotide, a tetrahydropyran modified nucleotide, a 1,5-anhydrohexitol modified nucleotide, a cyclohexenyl modified nucleotide, a nucleotide comprising a 5′-phosphorothioate group, a nucleotide comprising a 5′-methylphosphonate group, a nucleotide comprising a 5′ phosphate or 5′ phosphate mimic, a nucleotide comprising vinyl phosphonate, a nucleotide comprising adenosine-glycol nucleic acid (GNA), a nucleotide comprising thymidine-glycol nucleic acid (GNA)S-Isomer, a nucleotide comprising 2-hydroxymethyl-tetrahydrofurane-5-phosphate, a nucleotide comprising 2′-deoxythymidine-3′phosphate, a nucleotide comprising 2′-deoxyguanosine-3′-phosphate, a 2′-0 hexadecyl nucleotide, a nucleotide comprising a 2′-phosphate, a cytidine-2′-phosphate nucleotide, a guanosine-2′-phosphate nucleotide, a 2′-O-hexadecyl-cytidine-3′-phosphate nucleotide, a 2′-O-hexadecyl-adenosine-3′-phosphate nucleotide, a 2′-O-hexadecyl-guanosine-3′-phosphate nucleotide, a 2′-O-hexadecyl-uridine-3′-phosphate nucleotide, a a 5′-vinyl phosphonate (VP), a 2′-deoxyadenosine-3′-phosphate nucleotide, a 2′-deoxycytidine-3′-phosphate nucleotide, a 2′-deoxyguanosine-3′-phosphate nucleotide, a 2′-deoxythymidine-3′-phosphate nucleotide, a 2′-deoxyuridine nucleotide, and a terminal nucleotide linked to a cholesteryl derivative and a dodecanoic acid bisdecylamide group; and combinations thereof.

In one embodiment, at least one strand comprises a 3′ overhang of at least 1 nucleotide, or at least one strand comprises a 3′ overhang of at least 2 nucleotides.

Thee sense strand and the antisense strand may each independently be 15-30 nucleotides in length; each independently 19-30 nucleotides in length; each independently 19-25 nucleotides in length; each independently 19-23 nucleotides in length; or each independently 21-23 nucleotides in length.

The double stranded region may be 17-23 nucleotide pairs in length; 17-25 nucleotide pairs in length; 23-27 nucleotide pairs in length; 19-21 nucleotide pairs in length; or 21-23 nucleotide pairs in length.

In one embodiment, the double stranded RNAi agent further comprises at least one phosphorothioate or methylphosphonate internucleotide linkage.

In one embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at the 3′-terminus of one strand.

In another embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at the 5′-terminus of one strand.

In one embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at both the 5′- and the 3′-terminus of one strand.

In one embodiment, the double stranded RNAi agent comprises 6-8 phosphorothioate internucleotide linkages.

In one embodiment, the double stranded RNAi agent further comprises a ligand attached at the 3′-terminus of the sense strand.

In one embodiment, the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.

In one embodiment, the ligand is

In one embodiment, the dsRNA agent is conjugated to the ligand as shown in the following schematic

wherein X is O or S.

In one embodiment, substantially all of the nucleotides of said sense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification, wherein the sense strand comprises two phosphorothioate internucleotide linkages at the 5′-terminus, wherein substantially all of the nucleotides of said antisense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification, wherein the antisense strand comprises two phosphorothioate internucleotide linkages at the 5′ terminus and two phosphorothioate internucleotide linkages at the 3′-terminus, and wherein the sense strand is conjugated to one or more GalNAc derivatives attached through a branched bivalent or trivalent linker at the 3′-terminus.

In one embodiment, the sense strand differs by no more than 3 bases from the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand differs by no more than 3 bases from the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3 (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage.

In one embodiment, the sense strand differs by no more than 2 bases from the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand differs by no more than 2 bases from the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3′ (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage.

In one embodiment, the sense strand differs by no more than 1 base from the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand differs by no more than 1 base from the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3′ (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage.

In one embodiment, the sense strand comprises the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand comprises the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3′ (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage.

In one embodiment, the sense strand consists of the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand consists of the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3′ (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage.

In one embodiment, the sense strand comprises the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand comprises the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3′ (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage, and wherein a GalNAc ligand is conjugated to the 3′ end of the sense strand as shown in the following schematic:

wherein X is O.

In one embodiment, the sense strand consists of the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand consists of the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3′ (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage, and wherein a GalNAc ligand is conjugated to the 3′ end of the sense strand as shown in the following schematic:

wherein X is O.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the nucleotide sequence of Homo sapiens HAO1 mRNA (SEQ ID NO:1).

FIG. 2 shows the reverse complement of the nucleotide sequence of Homo sapiens HAO1 mRNA (SEQ ID NO:2).

FIG. 3 is a graph showing dose dependent inhibition of HAO1 mRNA by ALN-65585 in primary cyno hepatocytes.

FIG. 4 is two graphs showing HAO1 mRNA and serum glycolate levels following single does treatment with ALN-GO1 in mice.

FIG. 5 is a graph showing duration of HAO1 mRNA silencing following single dose treatment with ALN-GO1 in mice.

FIG. 6 is a graph showing HAO1 mRNA and serum glycolate levels following single dose treatment with ALN-GO1 in rats.

FIG. 7 is two graphs showing urinary oxalate and glycolate levels in a mouse model of primary hyperoxaluria type I after a single dose of ALN-GO1.

FIG. 8A is a graph showing HAO1 mRNA levels in a rat model of primary hyperoxaluria type I after a single dose of ALN-GO1.

FIG. 8B is a graph showing urinary oxalate levels in a rat model of primary hyperoxaluria type I after a single dose of ALN-GO1.

FIG. 9 is two graphs showing HAO1 mRNA and urinary oxalate levels in a rat model of primary hyperoxaluria type I after repeat dosing of ALN-GO1.

FIG. 10 is two graphs showing HAO1 mRNA and serum glycolate levels after repeat dosing in non-human primates.

FIG. 11 is a graph showing plasma glycolate levels in healthy human subjects treated with HAO1 siRNA ALN-GO1.

FIG. 12 is a graph showing plasma glycolate time to recovery in healthy human subjects treated with HAO1 siRNA ALN-GO1.

FIG. 13 is a graph showing 24 hour urine oxalate levels in Cohort 1 after administration of ALN-GO1.

FIG. 14 is a graph showing 24 hour urine oxalate levels in Cohort 2, 29 days after administration of ALN-GO1.

FIG. 15 is a graph showing reduction in urine oxalate levels in patients after administration of ALN-GO1.

FIG. 16 is a graph showing years after diagnosis vs ESRD.

FIG. 17 is a graph using a PK-PD model and showing a dose dependent increase in plasma glycolate levels.

FIG. 18 is a graph using the PK-PD model and describing the oxalate response in PH1 patients. Solid line=Median; Shaded area=5th-95th Percentile; Arrows=Dose administration; Symbols=Observations. Negative time values represents time prior to initiation of active ALN-GO1 dose regimen. Simulations were conducted assuming median baseline urinary oxalate of 1.7 (mmol/24 h/1.73 m²).

FIG. 19 is a graph using the PK-PD model and predicting the relationship between dosage and steady-state GO enzyme inhibition in PH1 patents. Solid lines=Median; Shaded area=5th-95th Percentile. Model estimated inhibition of glycolate oxidation rate and oxalate degradation rate are assumed to be same as GO enzyme inhibition.

FIG. 20 is a graph using the PK-PD model and predicting a relationship between dosage and steady-state urine oxalate reduction in PH1 patents. Dotted light line=1.5×ULN for oxalate: 0.7 mmol/24 h/1.73 m²; Dotted dark line=ULN for urinary oxalate: 0.46 mmol/24 h/1.73 m²; Solid lines=Median; Shaded area=5th-95th Percentile.

FIG. 21A is a graph showing renal stone event rates in PH1 patients ≥6 years old in the lumasirin and placebo arm of a randomized, double-blind, placebo-controlled study i) 12 months prior to consent, ii) after the 6 month double-blind period, and iii) after the 6 month extension period. Error bars represent 95% confidence intervals.

FIG. 21B is a graph showing renal stone event rates in PH1 patients ≥6 years old in the lumasirin arm of a randomized, double-blind, placebo-controlled study i) 12 months prior to consent, ii) after the 6 month double-blind period (Day 1-Month 6), iii) after the 6 month extension period (Month 6 to Month 12); iv) Month 12 to Month 18 in the extension period; and v) Month 18 to Month 24 in the extension period. Error bars represent 95% confidence intervals.

FIG. 22 is a graph showing nephrocalcinosis change from baseline in PH1 patients ≥6 years old in the lumasiran and placebo arm of a randomized, double-blind, placebo-controlled study after i) 6 months of placebo in the placebo arm, ii) 6 months of lumasiran in the lumasiran arm, and iii) 12 months of lumasiran in the lumasiran arm.

FIG. 23A is a graph showing renal stone event rates in PH1 patients <6 years old i) 12 months prior to consent, and ii) after 6 months of treatment with lumasiran. Error bars represent 95% confidence intervals. Annualized rate of renal stone events prior to consent was not calculated for patients <6 months old.

FIG. 23B is a graph showing renal stone event rates in PH1 patients <6 years old i) 12 months prior to consent, ii) after 6 months of treatment with lumasiran, and between 6 months and 12 months of treatment with lumasiran. Error bars represent 95% confidence intervals. Annualized rate of renal stone events prior to consent was not calculated for patients <6 months old.

FIG. 24 is a graph showing nephrocalcinosis change from baseline in PH1 patients <6 years old after 6 months of treatment with lumasiran.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods for inhibiting HAO1 expression. The present invention also provides methods for treating a subject having an HAO1 associated disorders, e.g., primary hyperoxaluria (PH), e.g., PH1, as well as methods for reducing plasma oxalate, reducing medullary nephrocalcinosis, and reducing systemic oxalosis in a subject having an HAO1 associated disorders, e.g., primary hyperoxaluria (PH), e.g., PH1. The methods include administering a double stranded RNAi agent, e.g., a double-stranded iRNA agent targeting HAO1, and compositions comprising such double stranded RNAi agents, in a dosing regimen which includes a loading phase and a maintenance phase.

The present inventors surprisingly discovered weight based dosing regimens, e.g., to treat, subjects having primary hyperoxaluria, e.g., PH1, that potently, durably, and effectively inhibit HAO1 expression, reduce plasma oxalate, reduce medullary nephrocalcinosis, and reduce systemic oxalosis, and achieve sufficient RISC loading. The present inventors have also surprisingly discovered that the weight based dosing regimens of the invention are effective regardless of whether the subject's kidney function is intact or impaired.

I. Definitions

In order that the present invention may be more readily understood, certain terms are first defined. In addition, it should be noted that whenever a value or range of values of a parameter are recited, it is intended that values and ranges intermediate to the recited values are also intended to be part of this invention.

The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element, e.g., a plurality of elements.

The term “including” is used herein to mean, and is used interchangeably with, the phrase “including but not limited to”.

The term “or” is used herein to mean, and is used interchangeably with, the term “and/or,” unless context clearly indicates otherwise.

The term “about” is used herein to mean within the typical ranges of tolerances in the art. For example, “about” can be understood as about 2 standard deviations from the mean. In certain embodiments, about means+10%. In certain embodiments, about means+5%. When about is present before a series of numbers or a range, it is understood that “about” can modify each of the numbers in the series or range.

The term “at least”, “no less than”, or “or more” prior to a number or series of numbers is understood to include the number adjacent to the term “at least”, and all subsequent numbers or integers that could logically be included, as clear from context. For example, the number of nucleotides in a nucleic acid molecule must be an integer. For example, “at least 19 nucleotides of a 21 nucleotide nucleic acid molecule” means that 19, 20, or 21 nucleotides have the indicated property. When at least is present before a series of numbers or a range, it is understood that “at least” can modify each of the numbers in the series or range.

As used herein, “no more than” or “or less” is understood as the value adjacent to the phrase and logical lower values or integers, as logical from context, to zero. For example, a duplex with an overhang of “no more than 2 nucleotides” has a 2, 1, or 0 nucleotide overhang. When “no more than” is present before a series of numbers or a range, it is understood that “no more than” can modify each of the numbers in the series or range. As used herein, ranges include both the upper and lower limit.

As used herein, methods of detection can include determination that the amount of analyte present is below the level of detection of the method.

In the event of a conflict between an indicated target site and the nucleotide sequence for a sense or antisense strand, the indicated sequence takes precedence.

In the event of a conflict between a sequence and its indicated site on a transcript or other sequence, the nucleotide sequence recited in the specification takes precedence.

As used herein, the term “primary hyperoxaluria” refers to a group of relatively rare autosomal recessive disorders of glyoxylate metabolism, which are characterized by markedly increased endogenous oxalate levels. There are three types of primary hyperoxalurias, which may be of type 1 (PH1), type 2 (PH2) and type 3. All three types are characterized by the inability to remove glyoxylate.

PH1, accounting for the majority of cases (70-80%), results from the absence or deficiency of the peroxisomal liver enzyme AGT, the activity of which depends on pyridoxal phosphate. As AGT catalyzes the transamination of glyoxylate to glycine, its deficiency in PH1 allows glyoxylate to be reduced to glycolate and to be oxidized to oxalate by the enzyme glycolate oxidase (GO), also known as hydroxyacid oxidase (HAO1).

PH2 results from the deficiency of the cytosolic liver enzyme glyoxylate reductase/hydroxypyruvate reductase (GRHPR). Severe hyperoxaluria is the clinical hallmark of PH1 and PH2, with reported urine oxalate levels ranging between 88 and 352 mg per 24 h (1-4 mmol per 24 h) for PH1 and 88 and 176 mg per 24 h (1-2 mmol per 24 h) for PH2.

In a third form of hyperoxaluria, PH3, patients present with normal AGT and GRHPR enzyme activities. Without wishing to be bound by a specific theory, it is believed that mutations in DHDPSL are responsible for PH3. It is assumed that DHDPSL encodes a 4-hydroxy-2-oxoglutarate aldolase which catalyzes the final step in the metabolism of hydroxyproline.

As used herein, “HAO1” refers to the gene encoding the enzyme hydroxyacid oxidase 1. Other gene names include GO, GOX, GOX1, and HAOX1. The protein is also known as glycolate oxidase and (S)-2-hydroxy-acid oxidase. The GenBank accession number of the human HAO1 mRNA is NM_017545.2; cynomolgous monkey (Macaca fascicularis) HAO1 mRNA is XM_005568381.1; Mouse (Mus musculus) HAO1 mRNA is NM_010403.2; Rat (Rattus norvegicus) HAO1 mRNA is XM_006235096.1.

Further information on HAO1 is provided, for example in the NCBI Gene database at https://www.ncbi.nlm.nih.gov/gene/54363.

The entire contents of each of the foregoing GenBank Accession numbers and the Gene database numbers are incorporated herein by reference as of the date of filing this application.

The term “HAO1,” as used herein, also refers to naturally occurring DNA sequence variations of the HAO1 gene, such as a single nucleotide polymorphism (SNP) in the HAO1 gene. Exemplary SNPs may be found in the NCBI dbSNP Short Genetic Variations database available at www.ncbi.nlm.nih.gov/projects/SNP.

As used herein, “target sequence” refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a HAO1 gene, including mRNA that is a product of RNA processing of a primary transcription product.

As used herein, the term “strand comprising a sequence” refers to an oligonucleotide comprising a chain of nucleotides that is described by the sequence referred to using the standard nucleotide nomenclature.

“G,” “C,” “A” and “U” each generally stand for a nucleotide that contains guanine, cytosine, adenine, and uracil as a base, respectively. “T” and “dT” are used interchangeably herein and refer to a deoxyribonucleotide wherein the nucleobase is thymine, e.g., deoxyribothymine, 2′-deoxythymidine or thymidine. However, it will be understood that the term “ribonucleotide” or “nucleotide” or “deoxyribonucleotide” can also refer to a modified nucleotide, as further detailed below, or a surrogate replacement moiety. The skilled person is well aware that guanine, cytosine, adenine, and uracil may be replaced by other moieties without substantially altering the base pairing properties of an oligonucleotide comprising a nucleotide bearing such replacement moiety. For example, without limitation, a nucleotide comprising inosine as its base may base pair with nucleotides containing adenine, cytosine, or uracil. Hence, nucleotides containing uracil, guanine, or adenine may be replaced in the nucleotide sequences of the invention by a nucleotide containing, for example, inosine.

Sequences comprising such replacement moieties are embodiments of the invention.

The terms “iRNA,” “RNAi agent,” “iRNA agent,” and “RNA interference agent” as used interchangeably herein, refer to an agent that contains RNA as that term is defined herein, and which mediates the targeted cleavage of an RNA transcript via an RNA-induced silencing complex (RISC) pathway. iRNA directs the sequence-specific degradation of mRNA through a process as RNA interference (RNAi). The iRNA modulates, e.g., inhibits, the expression of HAO1 in a cell, e.g., a cell within a subject, such as a mammalian subject.

In one embodiment, an RNAi agent of the invention includes a single stranded RNA that interacts with a target RNA sequence, e.g., a HAO1 target mRNA sequence, to direct the cleavage of the target RNA. Without wishing to be bound by theory, it is believed that long double stranded RNA introduced into cells is broken down into siRNA by a Type III endonuclease known as Dicer (Sharp et al. (2001) Genes Dev. 15:485). Dicer, a ribonuclease-III-like enzyme, processes the dsRNA into 19-23 base pair short interfering RNAs with characteristic two base 3′ overhangs (Bernstein, et al., (2001) Nature 409:363). The siRNAs are then incorporated into an RNA-induced silencing complex (RISC) where one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition (Nykanen, et al., (2001) Cell 107:309). Upon binding to the appropriate target mRNA, one or more endonucleases within the RISC cleave the target to induce silencing (Elbashir, et al., (2001) Genes Dev. 15:188). Thus, in one aspect the invention relates to a single stranded RNA (siRNA) generated within a cell and which promotes the formation of a RISC complex to effect silencing of the target gene, i.e., a HAO1 gene. Accordingly, the term “siRNA” is also used herein to refer to an RNAi as described above.

In another embodiment, the RNAi agent may be a single-stranded siRNA that is introduced into a cell or organism to inhibit a target mRNA. Single-stranded RNAi agents bind to the RISC endonuclease Argonaute 2, which then cleaves the target mRNA. The single-stranded siRNAs are generally 15-30 nucleotides and are chemically modified. The design and testing of single-stranded siRNAs are described in U.S. Pat. No. 8,101,348 and in Lima et al., (2012) Cell 150: 883-894, the entire contents of each of which are hereby incorporated herein by reference. Any of the antisense nucleotide sequences described herein may be used as a single-stranded siRNA as described herein or as chemically modified by the methods described in Lima et al., (2012) Cell 150: 883-894.

In yet another embodiment, the present invention provides single-stranded antisense oligonucleotide molecules targeting HAO1. A “single-stranded antisense oligonucleotide molecule” is complementary to a sequence within the target mRNA (i.e., HAO1). Single-stranded antisense oligonucleotide molecules can inhibit translation in a stoichiometric manner by base pairing to the mRNA and physically obstructing the translation machinery, see Dias, N. et al., (2002) Mol Cancer Ther 1:347-355. Alternatively, the single-stranded antisense oligonucleotide molecules inhibit a target mRNA by hydridizing to the target and cleaving the target through an RNaseH cleavage event. The single-stranded antisense oligonucleotide molecule may be about 10 to about 30 nucleotides in length and have a sequence that is complementary to a target sequence. For example, the single-stranded antisense oligonucleotide molecule may comprise a sequence that is at least about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more contiguous nucleotides from any one of the antisense nucleotide sequences described herein, or bind any of the target sites described herein. The single-stranded antisense oligonucleotide molecules may comprise modified RNA, DNA, or a combination thereof.

In another embodiment, an “iRNA” for use in the compositions, uses, and methods of the invention is a double-stranded RNA and is referred to herein as a “double stranded RNAi agent,” “double-stranded RNA (dsRNA) molecule,” “dsRNA agent,” or “dsRNA”. The term “dsRNA”, refers to a complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary nucleic acid strands, referred to as having “sense” and “antisense” orientations with respect to a target RNA, i.e., a HAO1 gene. In some embodiments of the invention, a double-stranded RNA (dsRNA) triggers the degradation of a target RNA, e.g., an mRNA, through a post-transcriptional gene-silencing mechanism referred to herein as RNA interference or RNAi.

In general, the majority of nucleotides of each strand of a dsRNA molecule are ribonucleotides, but as described in detail herein, each or both strands can also include one or more non-ribonucleotides, e.g., a deoxyribonucleotide and/or a modified nucleotide. In addition, as used in this specification, an “RNAi agent” may include ribonucleotides with chemical modifications; an RNAi agent may include substantial modifications at multiple nucleotides. Such modifications may include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a siRNA type molecule, are encompassed by “RNAi agent” for the purposes of this specification and claims.

The two strands forming the duplex structure may be different portions of one larger RNA molecule, or they may be separate RNA molecules. Where the two strands are part of one larger molecule, and therefore are connected by an uninterrupted chain of nucleotides between the 3′-end of one strand and the 5′-end of the respective other strand forming the duplex structure, the connecting RNA chain is referred to as a “hairpin loop.” Where the two strands are connected covalently by means other than an uninterrupted chain of nucleotides between the 3′-end of one strand and the 5′-end of the respective other strand forming the duplex structure, the connecting structure is referred to as a “linker.” The RNA strands may have the same or a different number of nucleotides. The maximum number of base pairs is the number of nucleotides in the shortest strand of the dsRNA minus any overhangs that are present in the duplex. In addition to the duplex structure, an RNAi agent may comprise one or more nucleotide overhangs.

In one embodiment, an RNAi agent of the invention is a dsRNA of 24-30 nucleotides that interacts with a target RNA sequence, e.g., a HAO1 target mRNA sequence, to direct the cleavage of the target RNA. Without wishing to be bound by theory, long double stranded RNA introduced into cells is broken down into siRNA by a Type III endonuclease known as Dicer (Sharp et al. (2001) Genes Dev. 15:485). Dicer, a ribonuclease-III-like enzyme, processes the dsRNA into 19-23 base pair short interfering RNAs with characteristic two base 3′ overhangs (Bernstein, et al., (2001) Nature 409:363). The siRNAs are then incorporated into an RNA-induced silencing complex (RISC) where one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition (Nykanen, et al., (2001) Cell 107:309). Upon binding to the appropriate target mRNA, one or more endonucleases within the RISC cleave the target to induce silencing (Elbashir, et al., (2001) Genes Dev. 15:188).

As used herein, a “nucleotide overhang” refers to the unpaired nucleotide or nucleotides that protrude from the duplex structure of an RNAi agent when a 3′-end of one strand of the RNAi agent extends beyond the 5′-end of the other strand, or vice versa. “Blunt” or “blunt end” means that there are no unpaired nucleotides at that end of the double stranded RNAi agent, i.e., no nucleotide overhang. A “blunt ended” RNAi agent is a dsRNA that is double-stranded over its entire length, i.e., no nucleotide overhang at either end of the molecule. The RNAi agents of the invention include RNAi agents with nucleotide overhangs at one end (i.e., agents with one overhang and one blunt end) or with nucleotide overhangs at both ends.

The term “antisense strand” refers to the strand of a double stranded RNAi agent which includes a region that is substantially complementary to a target sequence (e.g., a human HAO1 mRNA). As used herein, the term “region complementary to part of an mRNA encoding HAO1” refers to a region on the antisense strand that is substantially complementary to part of a HAO1 mRNA sequence. Where the region of complementarity is not fully complementary to the target sequence, the mismatches are most tolerated in the terminal regions and, if present, are generally in a terminal region or regions, e.g., within 6, 5, 4, 3, or 2 nucleotides of the 5′ and/or 3′ terminus.

The term “sense strand,” as used herein, refers to the strand of a dsRNA that includes a region that is substantially complementary to a region of the antisense strand.

As used herein, the term “cleavage region” refers to a region that is located immediately adjacent to the cleavage site. The cleavage site is the site on the target at which cleavage occurs. In some embodiments, the cleavage region comprises three bases on either end of, and immediately adjacent to, the cleavage site. In some embodiments, the cleavage region comprises two bases on either end of, and immediately adjacent to, the cleavage site. In some embodiments, the cleavage site specifically occurs at the site bound by nucleotides 10 and 11 of the antisense strand, and the cleavage region comprises nucleotides 11, 12 and 13.

As used herein, and unless otherwise indicated, the term “complementary,” when used to describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person. Such conditions can, for example, be stringent conditions, where stringent conditions may include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50° C. or 70° C. for 12-16 hours followed by washing. Other conditions, such as physiologically relevant conditions as may be encountered inside an organism, can apply. For example, a complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., RNAi. The skilled person will be able to determine the set of conditions most appropriate for a test of complementarity of two sequences in accordance with the ultimate application of the hybridized nucleotides.

Sequences can be “fully complementary” with respect to each when there is base-pairing of the nucleotides of the first nucleotide sequence with the nucleotides of the second nucleotide sequence over the entire length of the first and second nucleotide sequences. However, where a first sequence is referred to as “substantially complementary” with respect to a second sequence herein, the two sequences can be fully complementary, or they may form one or more, but generally not more than 4, 3 or 2 mismatched base pairs upon hybridization, while retaining the ability to hybridize under the conditions most relevant to their ultimate application. However, where two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity. For example, a dsRNA comprising one oligonucleotide 21 nucleotides in length and another oligonucleotide 23 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 21 nucleotides that is fully complementary to the shorter oligonucleotide, may yet be referred to as “fully complementary” for the purposes described herein.

“Complementary” sequences, as used herein, may also include, or be formed entirely from, non-Watson-Crick base pairs and/or base pairs formed from non-natural and modified nucleotides, in as far as the above requirements with respect to their ability to hybridize are fulfilled. Such non-Watson-Crick base pairs includes, but not limited to, G:U Wobble or Hoogstein base pairing.

The terms “complementary,” “fully complementary” and “substantially complementary” herein may be used with respect to the base matching between the sense strand and the antisense strand of a dsRNA, or between the antisense strand of a dsRNA and a target sequence, as will be understood from the context of their use.

As used herein, a polynucleotide that is “substantially complementary to at least part of” a messenger RNA (mRNA) refers to a polynucleotide that is substantially complementary to a contiguous portion of the mRNA of interest (e.g., an mRNA encoding HAO1) including a 5′ UTR, an open reading frame (ORF), or a 3′ UTR. For example, a polynucleotide is complementary to at least a part of a HAO1 mRNA if the sequence is substantially complementary to a non-interrupted portion of an mRNA encoding HAO1.

The phrase “contacting a cell with a double stranded RNAi agent,” as used herein, includes contacting a cell by any possible means. Contacting a cell with a double stranded RNAi agent includes contacting a cell in vitro with the RNAi agent or contacting a cell in vivo with the RNAi agent. The contacting may be done directly or indirectly. Thus, for example, the RNAi agent may be put into physical contact with the cell by the individual performing the method, or alternatively, the RNAi agent may be put into a situation that will permit or cause it to subsequently come into contact with the cell.

Contacting a cell in vitro may be done, for example, by incubating the cell with the RNAi agent. Contacting a cell in vivo may be done, for example, by injecting the RNAi agent into or near the tissue where the cell is located, or by injecting the RNAi agent into another area, the bloodstream or the subcutaneous space, such that the agent will subsequently reach the tissue where the cell to be contacted is located. For example, the RNAi agent may contain and/or be coupled to a ligand, e.g., a GalNAc3 ligand, that directs the RNAi agent to a site of interest, e.g., the liver. Combinations of in vitro and in vivo methods of contacting are also possible. In connection with the methods of the invention, a cell might also be contacted in vitro with an RNAi agent and subsequently transplanted into a subject.

As used herein, a “subject” includes a human or non-human animal, preferably a vertebrate, and more preferably a mammal. A subject may include a transgenic organism. Most preferably, the subject is a human, such as a human suffering from or predisposed to developing a HAO1 associated disorder.

A “patient” or “subject,” as used herein, is intended to include either a human or non-human animal, preferably a mammal, e.g., human or a monkey. Most preferably, the subject or patient is a human. In one embodiment, a “patient” or “subject” is a human pediatric subject or human pediatric patient. In another embodiment, a “patient” or “subject” is a human adult subject or human adult patient.

A “pediatric subject” or a “pediatric patient” as used herein are subjects between about 0 years of age to about 6 years or age and/or subjects having a body weight of about 20 kg or less. For example, such subjects can be 0-1, 0-2, 0-3, 0-4, 0-5, 1-2, 1-3, 1-4, 1-5, 1-6, 2-3, 2-4, 2-5, 2-6, 3-4, 3-5, 3-6, 4-5, 4-6 or 5-6 years old and may have a body weight of about 20 kg or less, 10 kg or less, 5 kg or less, 10-20 kg, 15-20 kg or 5-15 kg.

A “HAO1 associated disorder”, as used herein, is intended to include any disorder that can be treated or prevented, or the symptoms of which can be alleviated, by inhibiting the expression of HAO1. Examples include but are not limited to primary hyperoxaluria (PH), e.g., type 1 (PH1), type 2 (PH2), and type 3 (PH3). In one embodiment, the pPH is PH1.

“Therapeutically effective amount,” as used herein, is intended to include the amount of an RNAi agent that, when administered to a patient for treating a HAO1 associated disease, e.g., PH1, is sufficient to effect treatment of the disease (e.g., by diminishing, ameliorating or maintaining the existing disease or one or more symptoms of disease). The “therapeutically effective amount” may vary depending on the RNAi agent, how the agent is administered, the disease and its severity and the history, age, weight, family history, genetic makeup, stage of pathological processes mediated by HAO1 expression, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.

“Prophylactically effective amount,” as used herein, is intended to include the amount of an RNAi agent that, when administered to a subject who does not yet experience or display symptoms of a HAO1-associated disease, e.g., PH1, but who may be predisposed to the disease, is sufficient to prevent or ameliorate the disease or one or more symptoms of the disease. Ameliorating the disease includes slowing the course of the disease or reducing the severity of later-developing disease. The “prophylactically effective amount” may vary depending on the RNAi agent, how the agent is administered, the degree of risk of disease, and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.

As used herein, the terms “treating” or “treatment” refer to a beneficial or desired result including, but not limited to, alleviation or amelioration of one or more symptoms associated with unwanted HAO1 expression, e.g., hyperoxaluria, nephrocalcinosis, nephrolithiasis, and/or systemic oxalosis. “Treatment” can also mean prolonging survival as compared to expected survival in the absence of treatment.

As used herein, “prevention” or “preventing,” when used in reference to a disease, disorder or condition thereof, that would benefit from a reduction in expression of an HAO1 gene, refers to a reduction in the likelihood that a subject will develop a symptom associated with such a disease, disorder, or condition, e.g., a symptom associated with primary hyperoxaluria, e.g., hyperoxaluria, nephrocalcinosis, nephrolithiasis, and/or systemic oxalosis. The likelihood of developing hyperoxaluria, nephrocalcinosis, nephrolithiasis, and/or systemic oxalosis is reduced, for example, when an individual having one or more risk factors for hyperoxaluria, nephrocalcinosis, nephrolithiasis, and/or systemic oxalosis either fails to develop hyperoxaluria, nephrocalcinosis, nephrolithiasis, and/or systemic oxalosis or develops hyperoxaluria, nephrocalcinosis, nephrolithiasis, and/or systemic oxalosis with less severity relative to a population having the same risk factors and not receiving treatment as described herein. The failure to develop a disease, disorder or condition, or the reduction in the development of a symptom associated with such a disease, disorder or condition (e.g., by at least about 10% on a clinically accepted scale for that disease or disorder), or the exhibition of delayed symptoms delayed (e.g., by days, weeks, months or years) is considered effective prevention.

A “therapeutically-effective amount” or “prophylactically effective amount” also includes an amount of an RNAi agent that produces some desired local or systemic effect at a reasonable benefit/risk ratio applicable to any treatment. RNAi gents employed in the methods of the present invention may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.

The term “sample,” as used herein, includes a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject. Examples of biological fluids include blood, serum and serosal fluids, plasma, cerebrospinal fluid, ocular fluids, lymph, urine, saliva, and the like. Tissue samples may include samples from tissues, organs or localized regions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organs. In certain embodiments, samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g., hepatocytes). In some embodiments, a “sample derived from a subject” refers to blood or plasma drawn from the subject. In further embodiments, a “sample derived from a subject” refers to liver tissue (or subcomponents thereof) derived from the subject.

II. Methods of the Invention

The present invention provides methods for inhibiting expression of hydroxyacid oxidase (HAO1) in a human subject having primary hyperoxaluria (PH), e.g., primary hyperoxaluria type 1 (PH1). The methods include administering to the subject an RNAi agent, e.g., a double-stranded RNAi agent, targeting HAO1, as described herein.

The methods of the invention also include dosing regimens which include a loading phase “loading phase” of closely spaced administrations that may be followed by a “maintenance phase”, in which the RNAi agent is administered at longer spaced intervals. Such dosing regimens vary based on the weight of the subject at the initiation of treatment. Such dosing regimens are not varied based on the kidney function of the subject.

Accordingly, in one aspect, the present invention provides a method for inhibiting expression of hydroxyacid oxidase (HAO1) in a human subject having primary hyperoxaluria (PH), e.g., PH1). The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg, e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month, thereby inhibiting the expression of HAO1 in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for inhibiting expression of hydroxyacid oxidase (HAO1) in a human subject having primary hyperoxaluria. The method includes administering to the subject a therapeutically effective amount of a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of between about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg, e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 8 mg/kg, e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby inhibiting the expression of HAO1 in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In another aspect, the present invention provides a method for inhibiting expression of hydroxyacid oxidase (HAO1) in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby inhibiting the expression of HAO1 in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

Any of these schedules may optionally be repeated for one or more iterations. The number of iterations may depend on the achievement of a desired effect, e.g., the suppression of a HAO1 gene, and/or the achievement of a therapeutic or prophylactic effect, e.g., reducing oxalate levels or reducing a symptom of PH1.

The double stranded RNAi agent, or salt thereof, may be administered in a pharmaceutical composition.

The term “inhibiting,” as used herein, is used interchangeably with “reducing,” “silencing,” “downregulating” and other similar terms, and includes any level of inhibition.

The phrase “inhibiting expression of a HAO1” is intended to refer to inhibition of expression of any HAO1 gene (such as, e.g., a mouse HAO1 gene, a rat HAO1 gene, a monkey HAO1 gene, or a human HAO1 gene) as well as variants or mutants of a HAO1 gene. Thus, the HAO1 gene may be a wild-type HAO1 gene, a mutant HAO1 gene, or a transgenic HAO1 gene in the context of a genetically manipulated cell, group of cells, or organism.

“Inhibiting expression of a HAO1 gene” includes any level of inhibition of a HAO1 gene, e.g., at least partial suppression of the expression of a HAO1 gene. The expression of the HAO1 gene may be assessed based on the level, or the change in the level, of any variable associated with HAO1 gene expression, e.g., HAO1 mRNA level, HAO1 protein level. This level may be assessed in an individual cell or in a group of cells, including, for example, a sample derived from a subject.

Inhibition may be assessed by a decrease in an absolute or relative level of one or more variables that are associated with HAO1 expression compared with a control level. The control level may be any type of control level that is utilized in the art, e.g., a pre-dose baseline level, or a level determined from a similar subject, cell, or sample that is untreated or treated with a control (such as, e.g., buffer only control or inactive agent control).

In some embodiments of the methods of the invention, expression of a HAO1 gene is inhibited by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%. at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%.

Inhibition of the expression of a HAO1 gene may be manifested by a reduction of the amount of mRNA expressed by a first cell or group of cells (such cells may be present, for example, in a sample derived from a subject) in which a HAO1 gene is transcribed and which has or have been treated (e.g., by contacting the cell or cells with an RNAi agent of the invention, or by administering an RNAi agent of the invention to a subject in which the cells are or were present) such that the expression of a HAO1 gene is inhibited, as compared to a second cell or group of cells substantially identical to the first cell or group of cells but which has not or have not been so treated (control cell(s)). In some embodiments, the inhibition is assessed by expressing the level of mRNA in treated cells as a percentage of the level of mRNA in control cells, using the following formula:

$\frac{\left( {{mRNA}{in}{control}{cells}} \right) - \left( {{mRNA}{in}{treated}{cells}} \right)}{\left( {{mRNA}{in}{control}{cells}} \right)}{\bullet 100}\%$

Alternatively, inhibition of the expression of a HAO1 gene may be assessed in terms of a reduction of a parameter that is functionally linked to HAO1 gene expression, e.g., HAO1 protein expression, GO enzyme activity, urinary oxalate levels, plasma oxalate levels, plasma glycolate level, medullary nephrocalcinosis, systemic oxalosis, e.g., renal oxalosis, cardiac oxalosis, vascular oxalosis, skeletal oxalosis, dermatologic oxalosis, and ophthalmic oxalosis, e.g., cardiac oxalosis, and/or a hematological disorder, e.g., anemia.

For example, in some embodiments, inhibition of HAO1 expression is measured by plasma oxalate levels, e.g., using LC-MS/MS (liquid chromoatographytandem-mass spectrometry. In some embodiment, plasma oxalate levels of the subject are reduced by about 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more, or plasma oxalate levels are reduced to within normal range (<1.6 μmol/L) following administration.

In some embodiments, inhibition of HAO1 expression is assessed by determining the extent of medullary nephrocalcinosis. In one embodiment, medullary nephrocalcinosis is reduced following administration. As used herein, the term “reduced” with respect to medullary nephrocalcinosis includes a lowering or reduction in medullary nephrocalcinosis, e.g., from a baseline value, e.g., prior to treatment. “Reduced” with respect to medullary nephroclcinosis also includes no change in medullary nephrocalcinosis, e.g., from a baseline value, e.g., prior to treatment. In some embodiments, the extent of medullary nephrocalcinosis is lower (improved) than baseline, e.g., in one kidney or in both kidneys, and/or remains unchanged (no change) from baseline, e.g., in one kidney or in both kidneys. A skilled practitioner may readily assess medullary nephrocalcinosis by renal ultrasound. For example, as described in the Examples, an ultrasound measured the grade of medullary nephrocalcinosis (range: 0 to 3) where a higher grade indicated greater severity in medullary nephrocalcinosis. Changes in the grade of medullary nephrocalcinosis per kidney were categorized in 3 groups (1) no change, (2) worsening, or (3) improving.

In some embodiments, inhibition of HAO1 expression is is assessed by determining the extent of systemic oxalosis, renal oxalosis, cardiac oxalosis, vascular oxalosis, skeletal oxalosis, dermatologic oxalosis, and/or ophthalmic oxalosis, e.g., a change from baseline, e.g., a level prior to administration.

In some embodiments, cardiac oxalosis is assessed by echocardiogram (echo) and a cardiac function parameter, e.g., left ventricular ejection fraction (LVEF), global longitudinal strain (GLS) and/or early mitral inflow velocity:mitral annual early diastolic velocity (E/e′) is determined. In some embodiments, left ventricular ejection fraction (LVEF) is increased by at least about 5%, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50% or more; and/or global longitudinal strain (GLS) is decreased by at least about 2%, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10%, or more; and/or early mitral inflow velocity:mitral annual early diastolic velocity (E/e′) is increased by at least about 2%, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10%, or more following administration.

In some embodiments, dermatologic oxalosis is assessed using the Bates-Jensen Wound Assessment Tool. In some embodiments, the total score (1-60; 60 being wound deterioration, 13 being wound regeneration, and 1 being tissue health) on the Wound Status Continuum using the Bates-Jensen Wound Assessment Tool is reduced to about 55, 50, 45, 40, 35, 30, 25, 20, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1) following administration.

In some embodiments, ophthalmic oxalosis is assessed using total macular volume and visual acuity measurements. In some embodiments, total macular volume and visual acuity are increased following administration. A skilled practitioner may readily assess total macular volume and visual acuity by OCT (optical coherence tomography), CFP (color fundus photography; and/or FAF (Fundus autofluorescence).

In some embodiments, skeletal oxalosis is assessed by X-ray and/or nuclear imaging bone scan by a skilled practitioner. In some embodiments, skeletal oxalosis is decreased following administration.

In some embodiments, inhibition of HAO1 expression is assessed by determining a change in a hematologic disorder. For example, in some embodiments, subjects having PH systemic oxalosis may have bone marrow infiltration by oxalate crystals and, in some embodiments, renal failure and, as a result, anemia. Therefore, reducing systemic oxalosis using the methods of the invention will reduce oxalate in the bone marrow and improve hematopoiesis, thereby decreasing anemia in the subject. In some embodiments, white cell counts and platelet counts also improve.

In some embodiments, red blood cell counts are increased (and anemia decreased) following administration.

In some embodiments of the methods of the invention, HAO1 expression is decreased for an extended duration, e.g., at least one week, two weeks, three weeks, or four weeks or longer. For example, in certain instances, expression of the HAO1 gene is suppressed by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% by administration of an iRNA agent described herein.

In some embodiments, the HAO1 gene is suppressed by at least about 60%, 70%, or 80% by administration of the iRNA agent. In some embodiments, the HAO1 gene is suppressed by at least about 85%, 90%, or 95% by administration of the double-stranded oligonucleotide. In another embodiment, the HAO1 gene remains suppressed for 7 days, 10 days, 20 days, 30 days, or more following administration.

HAO1 gene silencing may be determined in any cell expressing HAO1, either constitutively or by genomic engineering, and by any assay known in the art. The liver is the major site of HAO1 expression. Other significant sites of expression include the kidneys and the uterus.

Inhibition of the expression of a HAO1 protein may be manifested by a reduction in the level of the HAO1 protein that is expressed by a cell or group of cells (e.g., the level of protein expressed in a sample derived from a subject). As explained above for the assessment of mRNA suppression, the inhibition of protein expression levels in a treated cell or group of cells may similarly be expressed as a percentage of the level of protein in a control cell or group of cells.

A control cell or group of cells that may be used to assess the inhibition of the expression of a HAO1 gene includes a cell or group of cells that has not yet been contacted with an RNAi agent of the invention. For example, the control cell or group of cells may be derived from an individual subject (e.g., a human or animal subject) prior to treatment of the subject with an RNAi agent.

The level of HAO1 mRNA that is expressed by a cell or group of cells may be determined using any method known in the art for assessing mRNA expression. In one embodiment, the level of expression of HAO1 in a sample is determined by detecting a transcribed polynucleotide, or portion thereof, e.g., mRNA of the HAO1 gene. RNA may be extracted from cells using RNA extraction techniques including, for example, using acid phenol/guanidine isothiocyanate extraction (RNAzol B; Biogenesis), RNeasy RNA preparation kits (Qiagen) or PAXgene (PreAnalytix, Switzerland). Typical assay formats utilizing ribonucleic acid hybridization include nuclear run-on assays, RT-PCR, RNase protection assays (Melton et al., Nuc. Acids Res. 12:7035), Northern blotting, in situ hybridization, and microarray analysis.

In one embodiment, the level of expression of HAO1 is determined using a nucleic acid probe. The term “probe”, as used herein, refers to any molecule that is capable of selectively binding to a specific HAO1. Probes can be synthesized by one of skill in the art, or derived from appropriate biological preparations. Probes may be specifically designed to be labeled. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molecules.

Isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, polymerase chain reaction (PCR) analyses and probe arrays. One method for the determination of mRNA levels involves contacting the isolated mRNA with a nucleic acid molecule (probe) that can hybridize to HAO1 mRNA. In one embodiment, the mRNA is immobilized on a solid surface and contacted with a probe, for example by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane, such as nitrocellulose. In an alternative embodiment, the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an Affymetrix gene chip array. A skilled artisan can readily adapt known mRNA detection methods for use in determining the level of HAO1 mRNA.

An alternative method for determining the level of expression of HAO1 in a sample involves the process of nucleic acid amplification and/or reverse transcriptase (to prepare cDNA) of for example mRNA in the sample, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88:189-193), self-sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), rolling circle replication (Lizardi et al., U.S. Pat. No. 5,854,033) or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers. In particular aspects of the invention, the level of expression of HAO1 is determined by quantitative fluorogenic RT-PCR (i.e., the TaqMan™ System).

The expression levels of HAO1 mRNA may be monitored using a membrane blot (such as used in hybridization analysis such as Northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are incorporated herein by reference. The determination of HAO1 expression level may also comprise using nucleic acid probes in solution.

In some embodiments, the level of mRNA expression is assessed using branched DNA (bDNA) assays or real time PCR (qPCR). The use of these methods is described and exemplified in the Examples presented herein.

The level of HAO1 protein expression may be determined using any method known in the art for the measurement of protein levels. Such methods include, for example, electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, fluid or gel precipitin reactions, absorption spectroscopy, a colorimetric assays, spectrophotometric assays, flow cytometry, immunodiffusion (single or double), immunoelectrophoresis, Western blotting, radioimmunoassay (RIA), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, electrochemiluminescence assays, and the like.

The term “sample” as used herein refers to a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject. Examples of biological fluids include blood, serum and serosal fluids, plasma, lymph, urine, cerebrospinal fluid, saliva, ocular fluids, and the like. Tissue samples may include samples from tissues, organs or localized regions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organs. In certain embodiments, samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g., hepatocytes). In some embodiments, a “sample derived from a subject” refers to blood or plasma drawn from the subject. In further embodiments, a “sample derived from a subject” refers to liver tissue derived from the subject.

In some embodiments of the methods of the invention, the RNAi agent is administered to a subject such that the RNAi agent is delivered to a specific site within the subject. The inhibition of expression of HAO1 may be assessed using measurements of the level or change in the level of HAO1 mRNA or HAO1 protein in a sample derived from fluid or tissue from the specific site within the subject. In some embodiments, the site is the liver. The site may also be a subsection or subgroup of cells from any one of the aforementioned sites. The site may also include cells that express a particular type of receptor.

The present invention also provides methods for treating or preventing diseases and conditions that can be modulated by HAO1 gene expression, such as primary hyperoxaluria (PH), e.g., PH1.

Accordingly, the present invention provides methods for treating subjects having primary hyperoxaluria (PH), e.g., primary hyperoxaluria type 1 (PH1). The methods include administering to the subject an RNAi agent, e.g., a double-stranded RNAi agent, targeting HAO1, as described herein. The methods may include administering to the subject a therapeutically or prophylactically effective amount of the double-stranded RNAi agent.

The treatment methods of the invention also include dosing regimens which include a loading phase “loading phase” of closely spaced administrations that may be followed by a “maintenance phase”, in which the RNAi agent is administered at longer spaced intervals. Such dosing regimens vary based on the weight of the subject at the initiation of treatment. Such dosing regimens are not varied based on the kidney function of the subject.

Accordingly, in one aspect, the present invention provides a method for treating a human subject having primary hyperoxaluria. The methods include administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg, e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month, thereby treating the human subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for treating a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg, e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 8 mg/kg, e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby treating the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one aspect, the present invention provides a method for treating a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby treating the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

Any of these schedules may optionally be repeated for one or more iterations. The number of iterations may depend on the achievement of a desired effect, e.g., the suppression of a HAO1 gene, and/or the achievement of a therapeutic or prophylactic effect, e.g., reducing oxalate levels or reducing a symptom of PH1.

The double stranded RNAi agent, or salt thereof, may be administered in a pharmaceutical composition.

In one embodiment, a dsRNA agent targeting HAO1 is administered to a subject having primary hyperoxaluria such that HAO1 levels, e.g., in a cell, tissue, blood, urine or other tissue or fluid of the subject are reduced by at least about 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 62%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99% or more and, subsequently, an additional therapeutic (as described below) is administered to the subject.

The additional therapeutic agent for the treatment of primary hyperoxaluria may be, for example, vitamin B6 (pyridoxine) and/or potassium citrate.

Administration of the dsRNA agent according to the methods and uses of the invention may result in a reduction of the severity, signs, symptoms, and/or markers of such diseases or disorders in a patient with primary hyperoxaluria. By “reduction” in this context is meant a statistically significant decrease in such level. The reduction can be, for example, at least about 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 100%.

Efficacy of treatment or prevention of disease can be assessed, for example by measuring disease progression, disease remission, symptom severity, reduction in pain, quality of life, dose of a medication required to sustain a treatment effect, level of a disease marker or any other measurable parameter appropriate for a given disease being treated or targeted for prevention. It is well within the ability of one skilled in the art to monitor efficacy of treatment or prevention by measuring any one of such parameters, or any combination of parameters. For example, efficacy of treatment of primary hyperoxaluria may be assessed, for example, by periodic monitoring of oxalate levels in the subject being treated. Comparisons of the later measurements with the initial measurements provide a physician an indication of whether the treatment is effective. It is well within the ability of one skilled in the art to monitor efficacy of treatment or prevention by measuring such a parameter, or any combination of parameters. In connection with the administration of a dsRNA agent targeting HAO1 or pharmaceutical composition thereof, “effective against” primary hyperoxaluria indicates that administration in a clinically appropriate manner results in a beneficial effect for at least a statistically significant fraction of patients, such as improvement of symptoms, a cure, a reduction in disease, extension of life, improvement in quality of life, or other effect generally recognized as positive by medical doctors familiar with treating primary hyperoxaluria and the related causes.

A treatment or preventive effect is evident when there is a statistically significant improvement in one or more parameters of disease status, or by a failure to worsen or to develop symptoms where they would otherwise be anticipated. As an example, a favorable change of at least 10% in a measurable parameter of disease, and preferably at least 20%, 30%, 40%, 50% or more can be indicative of effective treatment.

Any positive change resulting in e.g., lessening of severity of disease measured using the appropriate scale, represents adequate treatment using a dsRNA agent or dsRNA agent formulation as described herein.

For example, in some embodiments, efficacy of treatment is assessed by determining plasma glycolate level and/or urinary oxalate excretion and/or GO enzyme activity and/or plasma oxalate levels, e.g., a change from baseline, e.g., a level prior to administration.

In some embodiments, efficacy of treatment is assessed by determining plasma oxalate levels e.g., using LC-MS/MS (liquid chromoatographytandem-mass spectrometry. In some embodiment, plasma oxalate levels of the subject are reduced by about 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more, or plasma oxalate level is reduced to within normal range (<1.6 μmol/L) following administration.

In some embodiments, efficacy of treatment is assessed by determining the extent of medullary nephrocalcinosis. In one embodiment, medullary nephrocalcinosis is reduced following administration. As used herein, the term “reduced” with respect to medullary nephrocalcinosis includes a lowering or reduction in medullary nephrocalcinosis, e.g., from a baseline value, e.g., prior to treatment. “Reduced” with respect to medullary nephroclcinosis also includes no change in medullary nephrocalcinosis, e.g., from a baseline value, e.g., prior to treatment. In some embodiments, the extent of medullary nephrocalcinosis is lower (improved) than baseline, e.g., in one kidney or in both kidneys, and/or remains unchanged (no change) from baseline, e.g., in one kidney or in both kidneys. A skilled practitioner may readily assess medullary nephrocalcinosis by renal ultrasound. For example, as described in the Examples, an ultrasound measured the grade of medullary nephrocalcinosis (range: 0 to 3) where a higher grade indicated greater severity in medullary nephrocalcinosis. Changes in the grade of medullary nephrocalcinosis per kidney were categorized in 3 groups (1) no change, (2) worsening, or (3) improving.

In some embodiments, efficacy of treatment is assessed by determining the extent of systemic oxalosis, renal oxalosis, cardiac oxalosis, vascular oxalosis, skeletal oxalosis, dermatologic oxalosis, and/or ophthalmic oxalosis, e.g., a change from baseline, e.g., a level prior to administration.

In some embodiments, cardiac oxalosis is assessed by echocardiogram (echo) and a cardiac function parameter, e.g., left ventricular ejection fraction (LVEF), global longitudinal strain (GLS) and/or early mitral inflow velocity:mitral annual early diastolic velocity (E/e′) is determined. In some embodiments, left ventricular ejection fraction (LVEF) is increased by at least about 5%, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50% or more; and/or global longitudinal strain (GLS) is decreased by at least about 2%, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10%, or more; and/or early mitral inflow velocity:mitral annual early diastolic velocity (E/e′) is increased by at least about 2%, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10%, or more following administration.

In some embodiments, dermatologic oxalosis is assessed using the Bates-Jensen Wound Assessment Tool. In some embodiments, the total score (1-60; 60 being wound deterioration, 13 being would regeneration, and 1 being tissue health) on the Wound Status Continuum using the Bates-Jensen Wound Assessment Tool is reduced to about 55, 50, 45, 40, 35, 30, 25, 20, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1) following administration.

In some embodiments, ophthalmic oxalosis is assessed using total macular volume and visual acuity measurements. In some embodiments, total macular volume and visual acuity are increased following administration. A skilled practitioner may readily assess total macular volume and visual acuity by OCT (optical coherence tomography), CFP (color fundus photography; and/or FAF (Fundus autofluorescence).

In some embodiments, skeletal oxalosis is assessed by X-ray and/or nuclear imaging bone scan by a skilled practitioner. In some embodiments, skeletal oxalosis is decreased following administration.

In some embodiments, efficacy of treatment is assessed by determining a change in a hematologic disorder, e.g., a change from baseline, e.g., a level prior to administration. In some embodiment, red blood cell counts are increased (and anemia decreased) following administration.

The present invention further provides methods for reducing plasma oxalate in a human subject having primary hyperoxaluria (PH), e.g., primary hyperoxaluria type 1 (PH1); methods for reducing medullary nephrocalcinosis in a human subject having primary hyperoxaluria (PH), e.g., primary hyperoxaluria type 1 (PH1); and methods for reducing systemic oxalosis in a human subject having primary hyperoxaluria (PH), e.g., primary hyperoxaluria type 1 (PH1). The methods include administering to the subject an RNAi agent, e.g., a double-stranded RNAi agent, targeting HAO1, as described herein.

In some embodiments, the methods of the invention also include dosing regimens which include a loading phase “loading phase” of closely spaced administrations that may be followed by a “maintenance phase”, in which the RNAi agent is administered at longer spaced intervals. Such dosing regimens vary based on the weight of the subject at the initiation of treatment. Such dosing regimens are not varied based on the kidney function of the subject.

Accordingly, in one aspect, the present invention provides a method for reducing plasma oxalate in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month, thereby reducing plasma oxalate in the human subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for reducing plasma oxalate in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby reducing plasma oxalate in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In another aspect, the present invention provides a method for reducing plasma oxalate in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby reducing plasma oxalate in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

Plasma oxalate level may be reduced, e.g., a change from baseline, e.g., a level prior to administration, by about 35%, e.g., 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95%, or more following administration of the double stranded RNAi agent and/or reduced to within normal range following administration of the double stranded RNAi agent.

Any of these schedules may optionally be repeated for one or more iterations. The number of iterations may depend on the achievement of a desired effect.

The double stranded RNAi agent, or salt thereof, may be administered in a pharmaceutical composition.

In one aspect, the present invention provides a method for reducing medullary nephrocalcinosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month, thereby reducing medullary nephrocalcinosis in the human subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for reducing medullary nephrocalcinosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a therapeutically effective amount of a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby reducing medullary nephrocalcinosis in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In another aspect, the present invention provides a method for reducing medullary nephrocalcinosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby reducing medullary nephrocalcinosis in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

Medullary nephrocalcinosis may be reduced, e.g., the extent of medullary nephrocalcinosis is lower than baseline, e.g., in one kidney or in both kidneys, and/or remains unchanged from baseline, e.g., in one kidney or in both kidneys. A skilled practitioner may readily assess medullary nephrocalcinosis by renal ultrasound.

Any of these schedules may optionally be repeated for one or more iterations. The number of iterations may depend on the achievement of a desired effect.

The double stranded RNAi agent, or salt thereof, may be administered in a pharmaceutical composition.

In one aspect, the present invention provides a method for reducing systemic oxalosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month, thereby reducing systemic oxalosis in the human subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month.

In another aspect, the present invention provides a method for reducing systemic oxalosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a therapeutically effective amount of a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 8 mg/kg e.g., about 4, 4.5, 5, 5.5, 6, 6.5, 7. 7.5, or about 8 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby reducing systemic oxalosis in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

In one aspect, the present invention provides a method for reducing systemic oxalosis in a human subject having primary hyperoxaluria. The method includes administering to the subject a therapeutically effective amount of a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg, e.g., about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or about 5 mg/kg, of the double stranded RNAi agent, or salt thereof, to the subject about once every three months, thereby reducing systemic oxalosis in the subject having primary hyperoxaluria.

In one embodiment, the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months. In one embodiment, the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months.

The systemic oxalosis may be renal oxalosis, vascular oxalosis, cardiac oxalosis, bone oxalosis, and ophthalmic oxalosis.

In one embodiment, the systemic oxalosis is cardiac oxalosis. In one embodiment the systemic oxalosis is cardiac oxalosis and left ventricular ejection fraction (LVEF) is increased by at least about 5%, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50% or more, following administration of the double stranded RNAi agent.

In one embodiment the systemic oxalosis is cardiac oxalosis and global longitudinal strain (GLS) is decreased by at least about 2%, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10%, or more, following administration of the double stranded RNAi agent.

In one embodiment the systemic oxalosis is cardiac oxalosis and early mitral inflow velocity:mitral annual early diastolic velocity (E/e′) is increased by at least about 2%, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10%, following administration of the double stranded RNAi agent.

Any of these schedules may optionally be repeated for one or more iterations. The number of iterations may depend on the achievement of a desired effect.

The double stranded RNAi agent, or salt thereof, may be administered in a pharmaceutical composition.

In another aspect, the invention features, a method of instructing an end user, e.g., a caregiver or a subject, on how to administer an iRNA agent described herein. The method includes, optionally, providing the end user with one or more doses of the iRNA agent, and instructing the end user to administer the iRNA agent on a regimen described herein, thereby instructing the end user.

The in vivo methods and uses of the invention may include administering to a subject a composition containing a dsRNA agent, where the dsRNA agent includes a nucleotide sequence that is complementary to at least a part of an RNA transcript of the HAO1 gene of the mammal to be treated. When the organism to be treated is a mammal such as a human, the composition can be administered by any means known in the art including, but not limited to subcutaneous, intravenous, oral, intraperitoneal, or parenteral routes, including intracranial (e.g., intraventricular, intraparenchymal and intrathecal), intramuscular, transdermal, airway (aerosol), nasal, rectal, and topical (including buccal and sublingual) administration. In certain embodiments, the compositions are administered by subcutaneous or intravenous infusion or injection. In one embodiment, the compositions are administered by subcutaneous administration.

In some embodiments, the administration is via a depot injection. A depot injection may release the dsRNA agent in a consistent way over a prolonged time period. Thus, a depot injection may reduce the frequency of dosing needed to obtain a desired effect, e.g., a desired inhibition of HAO1, or a therapeutic or prophylactic effect. A depot injection may also provide more consistent serum concentrations. Depot injections may include subcutaneous injections or intramuscular injections. In preferred embodiments, the depot injection is a subcutaneous injection.

In some embodiments, the administration is via a pump. The pump may be an external pump or a surgically implanted pump. In certain embodiments, the pump is a subcutaneously implanted osmotic pump. In other embodiments, the pump is an infusion pump. An infusion pump may be used for intravenous, subcutaneous, arterial, or epidural infusions. In preferred embodiments, the infusion pump is a subcutaneous infusion pump. In other embodiments, the pump is a surgically implanted pump that delivers the dsRNA agent to the liver.

Other modes of administration include epidural, intracerebral, intracerebroventricular, nasal administration, intraarterial, intracardiac, intraosseous infusion, intrathecal, and intravitreal, and pulmonary. The mode of administration may be chosen based upon whether local or systemic treatment is desired and based upon the area to be treated. The route and site of administration may be chosen to enhance targeting.

In general, the iRNA agent does not activate the immune system, e.g., it does not increase cytokine levels, such as TNF-alpha or IFN-alpha levels. For example, when measured by an assay, such as an in vitro PBMC assay, such as described herein, the increase in levels of TNF-alpha or IFN-alpha, is less than 30%, 20%, or 10% of control cells treated with a control dsRNA, such as a dsRNA that does not target HAO1.

A patient in need of a HAO1 RNAi agent may be identified by taking a family history. A healthcare provider, such as a doctor, nurse, or family member, can take a family history before prescribing or administering a HAO1 dsRNA. A DNA test may also be performed on the patient to identify a mutation in the AGT1 gene, before a HAO1 RNAi agent is administered to the patient. Diagnosis of PH1 can be confirmed by any test well-known to one of skill in the art.

Owing to the inhibitory effects on HAO1 expression, a composition according to the invention or a pharmaceutical composition prepared therefrom can enhance the quality of life.

A dsRNA agent of the invention may be administered in “naked” form, or as a “free dsRNA agent.” A naked dsRNA agent is administered in the absence of a pharmaceutical composition. The naked dsRNA agent may be in a suitable buffer solution. The buffer solution may comprise acetate, citrate, prolamine, carbonate, or phosphate, or any combination thereof. In one embodiment, the buffer solution is phosphate buffered saline (PBS). The pH and osmolarity of the buffer solution containing the dsRNA agent can be adjusted such that it is suitable for administering to a subject.

Alternatively, a dsRNA agent of the invention may be administered as a pharmaceutical composition, such as a dsRNA agent liposomal formulation.

Subjects that would benefit from a reduction and/or inhibition of HAO1 gene expression are those having primary hyperoxaluria as described herein.

Treatment of a subject that would benefit from a reduction and/or inhibition of HAO1 gene expression includes therapeutic and prophylactic treatment (e.g., the subject carries a mutation in the AGTX gene and has PH1).

Suitable subjects may or may not have end-stage renal disease (ESRD). Suitable subject may or may not be on dialysis, e.g., hemodialysis.

The invention further provides methods and uses of a dsRNA agent or a pharmaceutical composition thereof (including methods and uses of a dsRNA agent or a pharmaceutical composition comprising a dsRNA agent for treatment of primary hyperoxaluria), in combination with other pharmaceuticals and/or other therapeutic methods, e.g., with known pharmaceuticals and/or known therapeutic methods, such as, for example, those which are currently employed for treating these disorders. For example, in certain embodiments, a dsRNA agent targeting HAO1 is administered in combination with, e.g., an agent useful in treating primary hyperoxaluria as described elsewhere herein.

For example, additional therapeutics and therapeutic methods suitable for treating a subject that would benefit from reduction in HAO1 expression, e.g., a subject having primary hyperoxaluria, include vitamin B6 (pyridoxine) and/or potassium citrate, or a combination of any of the foregoing.

The dsRNA agent (and/or agent(s) for treatment of primary hyperoxaluria) and an additional therapeutic agent and/or treatment may be administered at the same time and/or in the same combination, e.g., parenterally, or the additional therapeutic agent can be administered as part of a separate composition or at separate times and/or by another method known in the art or described herein.

III. Delivery of an iRNA Agent for Use in the Methods of the Invention

The delivery of an iRNA agent to a cell e.g., a cell within a subject, such as a human subject (e.g., a subject in need thereof, such as a subject having primary hyperoxaluria), for use in the methods of the invention, can be achieved in a number of different ways. For example, delivery may be performed by contacting a cell with an iRNA of the invention either in vitro or in vivo. In vivo delivery may also be performed directly by administering a composition comprising an iRNA, e.g., a dsRNA, to a subject. Alternatively, in vivo delivery may be performed indirectly by administering one or more vectors that encode and direct the expression of the iRNA. These alternatives are discussed further below.

In general, any method of delivering a nucleic acid molecule (in vitro or in vivo) can be adapted for use with an iRNA of the invention (see e.g., Akhtar S. and Julian R L. (1992) Trends Cell. Biol. 2(5):139-144 and WO94/02595, which are incorporated herein by reference in their entireties).

For in vivo delivery, factors to consider in order to deliver an iRNA molecule include, for example, biological stability of the delivered molecule, prevention of non-specific effects, and accumulation of the delivered molecule in the target tissue. The non-specific effects of an iRNA can be minimized by local administration, for example, by direct injection or implantation into a tissue or topically administering the preparation. Local administration to a treatment site maximizes local concentration of the agent, limits the exposure of the agent to systemic tissues that can otherwise be harmed by the agent or that can degrade the agent, and permits a lower total dose of the iRNA molecule to be administered. Several studies have shown successful knockdown of gene products when an iRNA is administered locally. For example, intraocular delivery of a VEGF dsRNA by intravitreal injection in cynomolgus monkeys (Tolentino, M J., et al (2004) Retina 24:132-138) and subretinal injections in mice (Reich, S J., et al (2003) Mol. Vis. 9:210-216) were both shown to prevent neovascularization in an experimental model of age-related macular degeneration. In addition, direct intratumoral injection of a dsRNA in mice reduces tumor volume (Pille, J., et al (2005) Mol. Ther. 11:267-274) and can prolong survival of tumor-bearing mice (Kim, W J., et al (2006) Mol. Ther. 14:343-350; Li, S., et al (2007) Mol. Ther. 15:515-523). RNA interference has also shown success with local delivery to the CNS by direct injection (Dorn, G., et al. (2004) Nucleic Acids 32:e49; Tan, P H., et al (2005) Gene Ther. 12:59-66; Makimura, H., et al (2002) BMC Neurosci. 3:18; Shishkina, G T., et al (2004) Neuroscience 129:521-528; Thakker, E R., et al (2004) Proc. Natl. Acad. Sci. U.S.A. 101:17270-17275; Akaneya, Y., et al (2005) J. Neurophysiol. 93:594-602) and to the lungs by intranasal administration (Howard, K A., et al (2006) Mol. Ther. 14:476-484; Zhang, X., et al (2004) J. Biol. Chem. 279:10677-10684; Bitko, V., et al (2005) Nat. Med. 11:50-55). For administering an iRNA systemically for the treatment of a disease, the RNA can be modified or alternatively delivered using a drug delivery system; both methods act to prevent the rapid degradation of the dsRNA by endo- and exo-nucleases in vivo. Modification of the RNA or the pharmaceutical carrier can also permit targeting of the iRNA composition to the target tissue and avoid undesirable off-target effects. iRNA molecules can be modified by chemical conjugation to lipophilic groups such as cholesterol to enhance cellular uptake and prevent degradation. For example, an iRNA directed against ApoB conjugated to a lipophilic cholesterol moiety was injected systemically into mice and resulted in knockdown of apoB mRNA in both the liver and jejunum (Soutschek, J., et al (2004) Nature 432:173-178). Conjugation of an iRNA to an aptamer has been shown to inhibit tumor growth and mediate tumor regression in a mouse model of prostate cancer (McNamara, J O., et al (2006) Nat. Biotechnol. 24:1005-1015). In an alternative embodiment, the iRNA can be delivered using drug delivery systems such as a nanoparticle, a dendrimer, a polymer, liposomes, or a cationic delivery system. Positively charged cationic delivery systems facilitate binding of an iRNA molecule (negatively charged) and also enhance interactions at the negatively charged cell membrane to permit efficient uptake of an iRNA by the cell. Cationic lipids, dendrimers, or polymers can either be bound to an iRNA, or induced to form a vesicle or micelle (see e.g., Kim S H., et al (2008) Journal of Controlled Release 129(2):107-116) that encases an iRNA. The formation of vesicles or micelles further prevents degradation of the iRNA when administered systemically. Methods for making and administering cationic-iRNA complexes are well within the abilities of one skilled in the art (see e.g., Sorensen, D R., et al (2003) J. Mol. Biol 327:761-766; Verma, U N., et al (2003) Clin. Cancer Res. 9:1291-1300; Arnold, A S et al (2007) J. Hypertens. 25:197-205, which are incorporated herein by reference in their entirety). Some non-limiting examples of drug delivery systems useful for systemic delivery of iRNAs include DOTAP (Sorensen, D R., et al (2003), supra; Verma, U N., et al (2003), supra), Oligofectamine, “solid nucleic acid lipid particles” (Zimmermann, T S., et al (2006) Nature 441:111-114), cardiolipin (Chien, P Y., et al (2005) Cancer Gene Ther. 12:321-328; Pal, A., et al (2005) Int J. Oncol. 26:1087-1091), polyethyleneimine (Bonnet M E., et al (2008) Pharm. Res. August 16 Epub ahead of print; Aigner, A. (2006) J. Biomed. Biotechnol. 71659), Arg-Gly-Asp (RGD) peptides (Liu, S. (2006) Mol. Pharm. 3:472-487), and polyamidoamines (Tomalia, D A., et al (2007) Biochem. Soc. Trans. 35:61-67; Yoo, H., et al (1999) Pharm. Res. 16:1799-1804). In some embodiments, an iRNA forms a complex with cyclodextrin for systemic administration. Methods for administration and pharmaceutical compositions of iRNAs and cyclodextrins can be found in U.S. Pat. No. 7,427,605, which is herein incorporated by reference in its entirety.

A. Vector Encoded iRNAs for Use in the Methods of the Invention

iRNA targeting the HAO1 gene can be expressed from transcription units inserted into DNA or RNA vectors (see, e.g., Couture, A, et al., TIG. (1996), 12:5-10; Skillern, A., et al., International PCT Publication No. WO 00/22113, Conrad, International PCT Publication No. WO 00/22114, and Conrad, U.S. Pat. No. 6,054,299). Expression can be transient (on the order of hours to weeks) or sustained (weeks to months or longer), depending upon the specific construct used and the target tissue or cell type. These transgenes can be introduced as a linear construct, a circular plasmid, or a viral vector, which can be an integrating or non-integrating vector. The transgene can also be constructed to permit it to be inherited as an extrachromosomal plasmid (Gassmann, et al., Proc. Natl. Acad. Sci. USA (1995) 92:1292).

The individual strand or strands of an iRNA can be transcribed from a promoter on an expression vector. Where two separate strands are to be expressed to generate, for example, a dsRNA, two separate expression vectors can be co-introduced (e.g., by transfection or infection) into a target cell. Alternatively each individual strand of a dsRNA can be transcribed by promoters both of which are located on the same expression plasmid. In one embodiment, a dsRNA is expressed as inverted repeat polynucleotides joined by a linker polynucleotide sequence such that the dsRNA has a stem and loop structure.

iRNA expression vectors are generally DNA plasmids or viral vectors. Expression vectors compatible with eukaryotic cells, preferably those compatible with vertebrate cells, can be used to produce recombinant constructs for the expression of an iRNA as described herein. Eukaryotic cell expression vectors are well known in the art and are available from a number of commercial sources. Typically, such vectors are provided containing convenient restriction sites for insertion of the desired nucleic acid segment. Delivery of iRNA expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that allows for introduction into a desired target cell.

iRNA expression plasmids can be transfected into target cells as a complex with cationic lipid carriers (e.g., Oligofectamine) or non-cationic lipid-based carriers (e.g., Transit-TKO™). Multiple lipid transfections for iRNA-mediated knockdowns targeting different regions of a target RNA over a period of a week or more are also contemplated by the invention. Successful introduction of vectors into host cells can be monitored using various known methods. For example, transient transfection can be signaled with a reporter, such as a fluorescent marker, such as Green Fluorescent Protein (GFP). Stable transfection of cells ex vivo can be ensured using markers that provide the transfected cell with resistance to specific environmental factors (e.g., antibiotics and drugs), such as hygromycin B resistance.

Viral vector systems which can be utilized with the methods and compositions described herein include, but are not limited to, (a) adenovirus vectors; (b) retrovirus vectors, including but not limited to lentiviral vectors, moloney murine leukemia virus, etc.; (c) adeno-associated virus vectors; (d) herpes simplex virus vectors; (e) SV 40 vectors; (f) polyoma virus vectors; (g) papilloma virus vectors; (h) picornavirus vectors; (i) pox virus vectors such as an orthopox, e.g., vaccinia virus vectors or avipox, e.g. canary pox or fowl pox; and (j) a helper-dependent or gutless adenovirus. Replication-defective viruses can also be advantageous. Different vectors will or will not become incorporated into the cells' genome. The constructs can include viral sequences for transfection, if desired. Alternatively, the construct can be incorporated into vectors capable of episomal replication, e.g. EPV and EBV vectors. Constructs for the recombinant expression of an iRNA will generally require regulatory elements, e.g., promoters, enhancers, etc., to ensure the expression of the iRNA in target cells. Other aspects to consider for vectors and constructs are further described below.

Vectors useful for the delivery of an iRNA will include regulatory elements (promoter, enhancer, etc.) sufficient for expression of the iRNA in the desired target cell or tissue. The regulatory elements can be chosen to provide either constitutive or regulated/inducible expression.

Expression of the iRNA can be precisely regulated, for example, by using an inducible regulatory sequence that is sensitive to certain physiological regulators, e.g., circulating glucose levels, or hormones (Docherty et al., 1994, FASEB J. 8:20-24). Such inducible expression systems, suitable for the control of dsRNA expression in cells or in mammals include, for example, regulation by ecdysone, by estrogen, progesterone, tetracycline, chemical inducers of dimerization, and isopropyl-beta-D1-thiogalactopyranoside (IPTG). A person skilled in the art would be able to choose the appropriate regulatory/promoter sequence based on the intended use of the iRNA transgene.

Viral vectors that contain nucleic acid sequences encoding an iRNA can be used. For example, a retroviral vector can be used (see Miller et al., Meth. Enzymol. 217:581-599 (1993)). These retroviral vectors contain the components necessary for the correct packaging of the viral genome and integration into the host cell DNA. The nucleic acid sequences encoding an iRNA are cloned into one or more vectors, which facilitate delivery of the nucleic acid into a patient. More detail about retroviral vectors can be found, for example, in Boesen et al., Biotherapy 6:291-302 (1994), which describes the use of a retroviral vector to deliver the mdr1 gene to hematopoietic stem cells in order to make the stem cells more resistant to chemotherapy. Other references illustrating the use of retroviral vectors in gene therapy are: Clowes et al., J. Clin. Invest. 93:644-651 (1994); Kiem et al., Blood 83:1467-1473 (1994); Salmons and Gunzberg, Human Gene Therapy 4:129-141 (1993); and Grossman and Wilson, Curr. Opin. in Genetics and Devel. 3:110-114 (1993). Lentiviral vectors contemplated for use include, for example, the HIV based vectors described in U.S. Pat. Nos. 6,143,520; 5,665,557; and 5,981,276, which are herein incorporated by reference.

Adenoviruses are also contemplated for use in delivery of iRNAs of the invention. Adenoviruses are especially attractive vehicles, e.g., for delivering genes to respiratory epithelia. Adenoviruses naturally infect respiratory epithelia where they cause a mild disease. Other targets for adenovirus-based delivery systems are liver, the central nervous system, endothelial cells, and muscle. Adenoviruses have the advantage of being capable of infecting non-dividing cells. Kozarsky and Wilson, Current Opinion in Genetics and Development 3:499-503 (1993) present a review of adenovirus-based gene therapy. Bout et al., Human Gene Therapy 5:3-10 (1994) demonstrated the use of adenovirus vectors to transfer genes to the respiratory epithelia of rhesus monkeys. Other instances of the use of adenoviruses in gene therapy can be found in Rosenfeld et al., Science 252:431-434 (1991); Rosenfeld et al., Cell 68:143-155 (1992); Mastrangeli et al., J. Clin. Invest. 91:225-234 (1993); PCT Publication WO94/12649; and Wang, et al., Gene Therapy 2:775-783 (1995). A suitable AV vector for expressing an iRNA featured in the invention, a method for constructing the recombinant AV vector, and a method for delivering the vector into target cells, are described in Xia H et al. (2002), Nat. Biotech. 20: 1006-1010.

Adeno-associated virus (AAV) vectors may also be used to delivery an iRNA of the invention (Walsh et al., Proc. Soc. Exp. Biol. Med. 204:289-300 (1993); U.S. Pat. No. 5,436,146). In one embodiment, the iRNA can be expressed as two separate, complementary single-stranded RNA molecules from a recombinant AAV vector having, for example, either the U6 or H1 RNA promoters, or the cytomegalovirus (CMV) promoter. Suitable AAV vectors for expressing the dsRNA featured in the invention, methods for constructing the recombinant AV vector, and methods for delivering the vectors into target cells are described in Samulski R et al. (1987), J. Virol. 61: 3096-3101; Fisher K J et al. (1996), J. Virol, 70: 520-532; Samulski R et al. (1989), J. Virol. 63: 3822-3826; U.S. Pat. Nos. 5,252,479; 5,139,941; International Patent Application No. WO 94/13788; and International Patent Application No. WO 93/24641, the entire disclosures of which are herein incorporated by reference.

Another viral vector suitable for delivery of an iRNA of the invention is a pox virus such as a vaccinia virus, for example an attenuated vaccinia such as Modified Virus Ankara (MVA) or NYVAC, an avipox such as fowl pox or canary pox.

The tropism of viral vectors can be modified by pseudotyping the vectors with envelope proteins or other surface antigens from other viruses, or by substituting different viral capsid proteins, as appropriate. For example, lentiviral vectors can be pseudotyped with surface proteins from vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and the like. AAV vectors can be made to target different cells by engineering the vectors to express different capsid protein serotypes; see, e.g., Rabinowitz J E et al. (2002), J Virol 76:791-801, the entire disclosure of which is herein incorporated by reference.

The pharmaceutical preparation of a vector can include the vector in an acceptable diluent, or can include a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system.

IV. Double Stranded iRNA Agents for Use in the Methods of the Invention

Suitable double-stranded RNAi agents for use on the methods of the invention include an antisense strand having a region of complementarity which is complementary to at least a part of an mRNA formed in the expression of a HAO1 gene. The region of complementarity is about 19-30 nucleotides in length (e.g., about 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, or 19 nucleotides in length). Upon contact with a cell expressing the HAO1 gene, the iRNA inhibits the expression of the gene (e.g., a human, a primate, a non-primate, or a rat HAO1 gene) by at least about 50% as assayed by, for example, a PCR or branched DNA (bDNA)-based method, or by a protein-based method, such as by immunofluorescence analysis, using, for example, western blotting or flow cytometric techniques. In preferred embodiments, inhibition of expression is determined by the qPCR method with the siRNA at a 10 nM concentration in an appropriate organism cell line provided therein. In preferred embodiments, inhibition of expression in vivo is determined by knockdown of the human gene in a rodent expressing the human gene, e.g., a mouse or an AAV-infected mouse expressing the human target gene, e.g., when administered a single dose, e.g., at 3 mg/kg at the nadir of RNA expression. RNA expression in liver is determined using the PCR methods.

A dsRNA includes two RNA strands that are complementary and hybridize to form a duplex structure under conditions in which the dsRNA will be used. One strand of a dsRNA (the antisense strand) includes a region of complementarity that is substantially complementary, and generally fully complementary, to a target sequence. The target sequence can be derived from the sequence of an mRNA formed during the expression of a HAO1 gene. The other strand (the sense strand) includes a region that is complementary to the antisense strand, such that the two strands hybridize and form a duplex structure when combined under suitable conditions. As described elsewhere herein and as known in the art, the complementary sequences of a dsRNA can also be contained as self-complementary regions of a single nucleic acid molecule, as opposed to being on separate oligonucleotides.

In some embodiment, the dsRNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand comprises at least 15 contiguous nucleotides differing by no more than 1, 2, or 3 nucleotides from the nucleotide sequence of any one of SEQ ID NOs:1, 12, and 14 and the antisense strand comprises at least 15 contiguous nucleotides differing by no more than 1, 2, or 3 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 2, 13, and 15.

Generally, the duplex structure is 19 to 30 base pairs in length. Similarly, the region of complementarity to the target sequence is 19 to 30 nucleotides in length.

In some embodiments, the dsRNA is about 19 to about 23 nucleotides in length, or about 25 to about 30 nucleotides in length. In general, the dsRNA is long enough to serve as a substrate for the Dicer enzyme. For example, it is well-known in the art that dsRNAs longer than about 21-23 nucleotides in length may serve as substrates for Dicer. As the ordinarily skilled person will also recognize, the region of an RNA targeted for cleavage will most often be part of a larger RNA molecule, often an mRNA molecule. Where relevant, a “part” of an mRNA target is a contiguous sequence of an mRNA target of sufficient length to allow it to be a substrate for RNAi-directed cleavage (i.e., cleavage through a RISC pathway).

One of skill in the art will also recognize that the duplex region is a primary functional portion of a dsRNA, e.g., a duplex region of about 19 to about 30 base pairs, e.g., about 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 base pairs. Thus, in one embodiment, to the extent that it becomes processed to a functional duplex, of e.g., 15-30 base pairs, that targets a desired RNA for cleavage, an RNA molecule or complex of RNA molecules having a duplex region greater than 30 base pairs is a dsRNA. Thus, an ordinarily skilled artisan will recognize that in one embodiment, a miRNA is a dsRNA. In another embodiment, a dsRNA is not a naturally occurring miRNA. In another embodiment, an iRNA agent useful to target expression of a HAO1 gene, is not generated in the target cell by cleavage of a larger dsRNA.

A dsRNA as described herein can further include one or more single-stranded nucleotide overhangs e.g., 1-4, 2-4, 1-3, 2-3, 1, 2, 3, or 4 nucleotides. dsRNAs having at least one nucleotide overhang can have superior inhibitory properties relative to their blunt-ended counterparts. A nucleotide overhang can comprise or consist of a nucleotide/nucleoside analog, including a deoxynucleotide/nucleoside. The overhang(s) can be on the sense strand, the antisense strand, or any combination thereof. Furthermore, the nucleotide(s) of an overhang can be present on the 5′-end, 3′-end, or both ends of an antisense or sense strand of a dsRNA.

The overhangs can be the result of one strand being longer than the other, or the result of two strands of the same length being staggered. The overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be another sequence. The first and second strands can also be joined, e.g., by additional bases to form a hairpin, or by other non-base linkers.

In one embodiment, the nucleotides in the overhang region of the RNAi agent can each independently be a modified or unmodified nucleotide including, but not limited to 2′-sugar modified, such as, 2-F, 2′-O-methyl, thymidine (T), 2

-O-methoxyethyl-5-methyluridine (Teo), 2

-O-methoxyethyladenosine (Aeo), 2′-O-methoxyethyl-5-methylcytidine (m5Ceo), and any combinations thereof. For example, TT can be an overhang sequence for either end on either strand. The overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be another sequence.

The 5′- or 3′-overhangs at the sense strand, antisense strand or both strands of the RNAi agent may be phosphorylated. In some embodiments, the overhang region(s) contains two nucleotides having a phosphorothioate between the two nucleotides, where the two nucleotides can be the same or different. In one embodiment, the overhang is present at the 3′-end of the sense strand, antisense strand, or both strands. In one embodiment, this 3′-overhang is present in the antisense strand. In one embodiment, this 3′-overhang is present in the sense strand.

The RNAi agent may contain only a single overhang, which can strengthen the interference activity of the RNAi, without affecting its overall stability. For example, the single-stranded overhang may be located at the 3′-terminal end of the sense strand or, alternatively, at the 3′-terminal end of the antisense strand. The RNAi may also have a blunt end, located at the 5′-end of the antisense strand (or the 3′-end of the sense strand) or vice versa. Generally, the antisense strand of the RNAi has a nucleotide overhang at the 3′-end, and the 5′-end is blunt. While not wishing to be bound by theory, the asymmetric blunt end at the 5′-end of the antisense strand and 3′-end overhang of the antisense strand favor the guide strand loading into RISC process.

In some embodiments, the double-stranded RNAi agents for use in the methods of the present invention are unmodified. In other embodiments, the double-stranded RNAi agents for use in the methods of the present invention are modified, e.g., comprise chemical modifications capable of inhibiting the expression of a target gene (i.e., a HAO1 gene) in vivo.

As described in more detail below, in certain aspects of the invention, substantially all of the nucleotides of an iRNA of the invention are modified. In other embodiments of the invention, all of the nucleotides of an iRNA of the invention are modified. iRNAs of the invention in which “substantially all of the nucleotides are modified” are largely but not wholly modified and can include not more than 5, 4, 3, 2, or 1 unmodified nucleotides.

Any of the nucleic acids, e.g., RNAi, featured in the invention can be synthesized and/or modified by methods well established in the art, such as those described in “Current protocols in nucleic acid chemistry,” Beaucage, S. L. et al. (Edrs.), John Wiley & Sons, Inc., New York, NY, USA, which is hereby incorporated herein by reference. Modifications include, for example, end modifications, e.g., 5′-end modifications (phosphorylation, conjugation, inverted linkages) or 3′-end modifications (conjugation, DNA nucleotides, inverted linkages, etc.); base modifications, e.g., replacement with stabilizing bases, destabilizing bases, or bases that base pair with an expanded repertoire of partners, removal of bases (abasic nucleotides), or conjugated bases; sugar modifications (e.g., at the 2′-position or 4′-position) or replacement of the sugar; and/or backbone modifications, including modification or replacement of the phosphodiester linkages. Specific examples of iRNA compounds useful in the embodiments described herein include, but are not limited to RNAs containing modified backbones or no natural internucleoside linkages. RNAs having modified backbones include, among others, those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified RNAs that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides. In some embodiments, a modified iRNA will have a phosphorus atom in its internucleoside backbone.

Modified RNA backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′ linkages, 2′-5′-linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixed salts and free acid forms are also included.

Representative U.S. patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,195; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,316; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,625,050; 6,028,188; 6,124,445; 6,160,109; 6,169,170; 6,172,209; 6,239,265; 6,277,603; 6,326,199; 6,346,614; 6,444,423; 6,531,590; 6,534,639; 6,608,035; 6,683,167; 6,858,715; 6,867,294; 6,878,805; 7,015,315; 7,041,816; 7,273,933; 7,321,029; and U.S. Pat. RE39464, the entire contents of each of which are hereby incorporated herein by reference.

Modified RNA backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂ component parts.

Representative U.S. patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 564,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and, 5,677,439, the entire contents of each of which are hereby incorporated herein by reference.

In other embodiments, suitable RNA mimetics are contemplated for use in iRNAs, in which both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an RNA mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar backbone of an RNA is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative U.S. patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, the entire contents of each of which are hereby incorporated herein by reference. Additional PNA compounds suitable for use in the iRNAs of the invention are described in, for example, in Nielsen et al., Science, 1991, 254, 1497-1500.

Some embodiments featured in the invention include RNAs with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular —CH₂—NH—CH₂—, —CH₂—N(CH₃)—O—CH₂— [known as a methylene (methylimino) or MMI backbone], —CH₂—O—N(CH₃)—CH₂—, —CH₂—N(CH₃)—N(CH₃)—CH₂— and —N(CH₃)—CH₂—CH₂— [wherein the native phosphodiester backbone is represented as —O—P—O—CH₂—] of the above-referenced U.S. Pat. No. 5,489,677, and the amide backbones of the above-referenced U.S. Pat. No. 5,602,240. In some embodiments, the RNAs featured herein have morpholino backbone structures of the above-referenced U.S. Pat. No. 5,034,506.

Modified RNAs can also contain one or more substituted sugar moieties. The iRNAs, e.g., dsRNAs, featured herein can include one of the following at the 2′-position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl can be substituted or unsubstituted C₁ to C₁₀ alkyl or C₂ to C₁₀ alkenyl and alkynyl. Exemplary suitable modifications include O[(CH₂)_(n)O]_(m)CH₃, O(CH₂)·_(n)OCH₃, O(CH₂)·NH₂, O(CH₂)_(n)CH₃, O(CH₂)_(n)ONH₂, and O(CH₂)_(n)ON[(CH₂)_(n)CH₃)]₂, where n and m are from 1 to about 10. In other embodiments, dsRNAs include one of the following at the 2′ position: C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an iRNA, or a group for improving the pharmacodynamic properties of an iRNA, and other substituents having similar properties. In some embodiments, the modification includes a 2′-methoxyethoxy (2′-O—CH₂CH₂OCH₃, also known as 2′-O-(2-methoxyethyl) or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78:486-504) i.e., an alkoxy-alkoxy group. Another exemplary modification is 2′-dimethylaminooxyethoxy, i.e., a O(CH₂)₂ON(CH₃)₂ group, also known as 2′-DMAOE, as described in examples herein below, and 2′-dimethylaminoethoxyethoxy (also known in the art as 2′-O-dimethylaminoethoxyethyl or 2′-DMAEOE), i.e., 2′-O—CH₂—O—CH₂—N(CH₂)₂.

Other modifications include 2′-methoxy (2′-OCH₃), 2′-aminopropoxy (2′-OCH₂CH₂CH₂NH₂) and 2′-fluoro (2′-F). Similar modifications can also be made at other positions on the RNA of an iRNA, particularly the 3′ position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linked dsRNAs and the 5′ position of 5′ terminal nucleotide. iRNAs can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative U.S. patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, certain of which are commonly owned with the instant application. The entire contents of each of the foregoing are hereby incorporated herein by reference.

An iRNA can also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as deoxy-thymine (dT), 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl anal other 8-substituted adenines and guanines, 5-halo, particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-daazaadenine and 3-deazaguanine and 3-deazaadenine. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in Modified Nucleosides in Biochemistry, Biotechnology and Medicine, Herdewijn, P. ed. Wiley-VCH, 2008; those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. L, ed. John Wiley & Sons, 1990, these disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y S., Chapter 15, dsRNA Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., Ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds featured in the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., Eds., dsRNA Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are exemplary base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.

Representative U.S. patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Pat. Nos. 3,687,808, 4,845,205; 513,030; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; 5,681,941; 5,750,692; 6,015,886; 6,147,200; 6,166,197; 6,222,025; 6,235,887; 6,380,368; 6,528,640; 6,639,062; 6,617,438; 7,045,610; 7,427,672; and 7,495,088, the entire contents of each of which are hereby incorporated herein by reference.

The RNA of an iRNA can also be modified to include one or more locked nucleic acids (LNA). A locked nucleic acid is a nucleotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2′ and 4′ carbons. This structure effectively “locks” the ribose in the 3′-endo structural conformation. The addition of locked nucleic acids to siRNAs has been shown to increase siRNA stability in serum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33(1):439-447; Mook, O R. et al., (2007) Mol Canc Ther 6(3):833-843; Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193).

Representative U.S. Patents that teach the preparation of locked nucleic acid nucleotides include, but are not limited to, the following: U.S. Pat. Nos. 6,268,490; 6,670,461; 6,794,499; 6,998,484; 7,053,207; 7,084,125; and 7,399,845, the entire contents of each of which are hereby incorporated herein by reference.

Potentially stabilizing modifications to the ends of RNA molecules can include N-(acetylaminocaproyl)-4-hydroxyprolinol (Hyp-C6-NHAc), N-(caproyl-4-hydroxyprolinol (Hyp-C6), N-(acetyl-4-hydroxyprolinol (Hyp-NHAc), thymidine-2′-O-deoxythymidine (ether), N-(aminocaproyl)-4-hydroxyprolinol (Hyp-C6-amino), 2-docosanoyl-uridine-3″-phosphate, inverted base dT(idT) and others. Disclosure of this modification can be found in PCT Publication No. WO 2011/005861.

A. Modified iRNAs Comprising Motifs of the Invention

In certain aspects of the invention, the double-stranded RNAi agents of the invention include agents with chemical modifications as disclosed, for example, in U.S. Provisional Application No. 61/561,710, filed on Nov. 18, 2011, or in PCT/US2012/065691, filed on Nov. 16, 2012, and published as WO2013075035 A1, the entire contents of each of which are incorporated herein by reference.

As shown herein and in Provisional Application No. 61/561,710, a superior result may be obtained by introducing one or more motifs of three identical modifications on three consecutive nucleotides into a sense strand and/or antisense strand of a RNAi agent, particularly at or near the cleavage site. In some embodiments, the sense strand and antisense strand of the RNAi agent may otherwise be completely modified. The introduction of these motifs interrupts the modification pattern, if present, of the sense and/or antisense strand. The RNAi agent may be optionally conjugated with a GalNAc derivative ligand, for instance on the sense strand. The resulting RNAi agents present superior gene silencing activity.

More specifically, it has been surprisingly discovered that when the sense strand and antisense strand of the double-stranded RNAi agent are modified to have one or more motifs of three identical modifications on three consecutive nucleotides at or near the cleavage site of at least one strand of an RNAi agent, the gene silencing activity of the RNAi agent was superiorly enhanced.

In one embodiment, the RNAi agent is a double ended bluntmer of 19 nucleotides in length, wherein the sense strand contains at least one motif of three 2′-F modifications on three consecutive nucleotides at positions 7, 8, 9 from the 5′end. The antisense strand contains at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5′end.

In another embodiment, the RNAi agent is a double ended bluntmer of 20 nucleotides in length, wherein the sense strand contains at least one motif of three 2′-F modifications on three consecutive nucleotides at positions 8, 9, 10 from the 5′end. The antisense strand contains at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5′end.

In yet another embodiment, the RNAi agent is a double ended bluntmer of 21 nucleotides in length, wherein the sense strand contains at least one motif of three 2′-F modifications on three consecutive nucleotides at positions 9, 10, 11 from the 5′end. The antisense strand contains at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5′end.

In one embodiment, the RNAi agent comprises a 21 nucleotide sense strand and a 23 nucleotide antisense strand, wherein the sense strand contains at least one motif of three 2′-F modifications on three consecutive nucleotides at positions 9, 10, 11 from the 5′end; the antisense strand contains at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5′end, wherein one end of the RNAi agent is blunt, while the other end comprises a 2 nucleotide overhang. Preferably, the 2 nucleotide overhang is at the 3′-end of the antisense strand. When the 2 nucleotide overhang is at the 3′-end of the antisense strand, there may be two phosphorothioate internucleotide linkages between the terminal three nucleotides, wherein two of the three nucleotides are the overhang nucleotides, and the third nucleotide is a paired nucleotide next to the overhang nucleotide. In one embodiment, the RNAi agent additionally has two phosphorothioate internucleotide linkages between the terminal three nucleotides at both the 5′-end of the sense strand and at the 5′-end of the antisense strand. In one embodiment, every nucleotide in the sense strand and the antisense strand of the RNAi agent, including the nucleotides that are part of the motifs are modified nucleotides. In one embodiment each residue is independently modified with a 2′-O-methyl or 3′-fluoro, e.g., in an alternating motif. Optionally, the RNAi agent further comprises a ligand (preferably GalNAc₃).

In one embodiment, the RNAi agent comprises sense and antisense strands, wherein the RNAi agent comprises a first strand having a length which is at least 25 and at most 29 nucleotides and a second strand having a length which is at most 30 nucleotides with at least one motif of three 2′-O-methyl modifications on three consecutive nucleotides at position 11, 12, 13 from the 5′ end; wherein the 3′ end of the first strand and the 5′ end of the second strand form a blunt end and the second strand is 1-4 nucleotides longer at its 3′ end than the first strand, wherein the duplex region which is at least 25 nucleotides in length, and the second strand is sufficiently complementary to a target mRNA along at least 19 nucleotide of the second strand length to reduce target gene expression when the RNAi agent is introduced into a mammalian cell, and wherein dicer cleavage of the RNAi agent preferentially results in an siRNA comprising the 3′ end of the second strand, thereby reducing expression of the target gene in the mammal. Optionally, the RNAi agent further comprises a ligand.

In one embodiment, the sense strand of the RNAi agent contains at least one motif of three identical modifications on three consecutive nucleotides, where one of the motifs occurs at the cleavage site in the sense strand.

In one embodiment, the antisense strand of the RNAi agent can also contain at least one motif of three identical modifications on three consecutive nucleotides, where one of the motifs occurs at or near the cleavage site in the antisense strand

For an RNAi agent having a duplex region of 17-23 nucleotides in length, the cleavage site of the antisense strand is typically around the 10, 11 and 12 positions from the 5′-end. Thus the motifs of three identical modifications may occur at the 9, 10, 11 positions; 10, 11, 12 positions; 11, 12, 13 positions; 12, 13, 14 positions; or 13, 14, 15 positions of the antisense strand, the count starting from the 1^(st) nucleotide from the 5′-end of the antisense strand, or, the count starting from the 1^(st) paired nucleotide within the duplex region from the 5′-end of the antisense strand. The cleavage site in the antisense strand may also change according to the length of the duplex region of the RNAi from the 5′-end.

The sense strand of the RNAi agent may contain at least one motif of three identical modifications on three consecutive nucleotides at the cleavage site of the strand; and the antisense strand may have at least one motif of three identical modifications on three consecutive nucleotides at or near the cleavage site of the strand. When the sense strand and the antisense strand form a dsRNA duplex, the sense strand and the antisense strand can be so aligned that one motif of the three nucleotides on the sense strand and one motif of the three nucleotides on the antisense strand have at least one nucleotide overlap, i.e., at least one of the three nucleotides of the motif in the sense strand forms a base pair with at least one of the three nucleotides of the motif in the antisense strand. Alternatively, at least two nucleotides may overlap, or all three nucleotides may overlap.

In one embodiment, the sense strand of the RNAi agent may contain more than one motif of three identical modifications on three consecutive nucleotides. The first motif may occur at or near the cleavage site of the strand and the other motifs may be a wing modification. The term “wing modification” herein refers to a motif occurring at another portion of the strand that is separated from the motif at or near the cleavage site of the same strand. The wing modification is either adjacent to the first motif or is separated by at least one or more nucleotides. When the motifs are immediately adjacent to each other than the chemistry of the motifs are distinct from each other and when the motifs are separated by one or more nucleotide than the chemistries can be the same or different. Two or more wing modifications may be present. For instance, when two wing modifications are present, each wing modification may occur at one end relative to the first motif which is at or near cleavage site or on either side of the lead motif.

Like the sense strand, the antisense strand of the RNAi agent may contain more than one motifs of three identical modifications on three consecutive nucleotides, with at least one of the motifs occurring at or near the cleavage site of the strand. This antisense strand may also contain one or more wing modifications in an alignment similar to the wing modifications that may be present on the sense strand.

In one embodiment, the wing modification on the sense strand or antisense strand of the RNAi agent typically does not include the first one or two terminal nucleotides at the 3′-end, 5′-end or both ends of the strand.

In another embodiment, the wing modification on the sense strand or antisense strand of the RNAi agent typically does not include the first one or two paired nucleotides within the duplex region at the 3′-end, 5′-end or both ends of the strand.

When the sense strand and the antisense strand of the RNAi agent each contain at least one wing modification, the wing modifications may fall on the same end of the duplex region, and have an overlap of one, two or three nucleotides.

When the sense strand and the antisense strand of the RNAi agent each contain at least two wing modifications, the sense strand and the antisense strand can be so aligned that two modifications each from one strand fall on one end of the duplex region, having an overlap of one, two or three nucleotides; two modifications each from one strand fall on the other end of the duplex region, having an overlap of one, two or three nucleotides; two modifications one strand fall on each side of the lead motif, having an overlap of one, two or three nucleotides in the duplex region.

In one embodiment, every nucleotide in the sense strand and antisense strand of the RNAi agent, including the nucleotides that are part of the motifs, may be modified. Each nucleotide may be modified with the same or different modification which can include one or more alteration of one or both of the non-linking phosphate oxygens and/or of one or more of the linking phosphate oxygens; alteration of a constituent of the ribose sugar, e.g., of the 2′ hydroxyl on the ribose sugar; wholesale replacement of the phosphate moiety with “dephospho” linkers; modification or replacement of a naturally occurring base; and replacement or modification of the ribose-phosphate backbone.

As nucleic acids are polymers of subunits, many of the modifications occur at a position which is repeated within a nucleic acid, e.g., a modification of a base, or a phosphate moiety, or a non-linking O of a phosphate moiety. In some cases the modification will occur at all of the subject positions in the nucleic acid but in many cases it will not. By way of example, a modification may only occur at a 3′ or 5′ terminal position, may only occur in a terminal region, e.g., at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand. A modification may occur in a double strand region, a single strand region, or in both. A modification may occur only in the double strand region of a RNA or may only occur in a single strand region of a RNA. For example, a phosphorothioate modification at a non-linking O position may only occur at one or both termini, may only occur in a terminal region, e.g., at a position on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand, or may occur in double strand and single strand regions, particularly at termini. The 5′ end or ends can be phosphorylated.

It may be possible, e.g., to enhance stability, to include particular bases in overhangs, or to include modified nucleotides or nucleotide surrogates, in single strand overhangs, e.g., in a 5′ or 3′ overhang, or in both. For example, it can be desirable to include purine nucleotides in overhangs. In some embodiments all or some of the bases in a 3′ or 5′ overhang may be modified, e.g., with a modification described herein. Modifications can include, e.g., the use of modifications at the 2′ position of the ribose sugar with modifications that are known in the art, e.g., the use of deoxyribonucleotides, 2′-deoxy-2′-fluoro (2′-F) or 2′-O-methyl modified instead of the ribosugar of the nucleobase, and modifications in the phosphate group, e.g., phosphorothioate modifications. Overhangs need not be homologous with the target sequence.

In one embodiment, each residue of the sense strand and antisense strand is independently modified with LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O-methyl, 2′-O-allyl, 2′-C-allyl, 2′-deoxy, 2′-hydroxyl, or 2′-fluoro. The strands can contain more than one modification. In one embodiment, each residue of the sense strand and antisense strand is independently modified with 2′-O-methyl or 2′-fluoro.

At least two different modifications are typically present on the sense strand and antisense strand. Those two modifications may be the 2′-O-methyl or 2′-fluoro modifications, or others.

In one embodiment, the N_(a) and/or N_(b) comprise modifications of an alternating pattern. The term “alternating motif” as used herein refers to a motif having one or more modifications, each modification occurring on alternating nucleotides of one strand. The alternating nucleotide may refer to one per every other nucleotide or one per every three nucleotides, or a similar pattern. For example, if A, B and C each represent one type of modification to the nucleotide, the alternating motif can be “ABABABABABAB . . . ,” “AABBAABBAABB . . . ,” “AABAABAABAAB . . . ,” “AAABAAABAAAB . . . ,” “AAABBBAAABBB . . . ,” or “ABCABCABCABC . . . ,” etc.

The type of modifications contained in the alternating motif may be the same or different. For example, if A, B, C, D each represent one type of modification on the nucleotide, the alternating pattern, i.e., modifications on every other nucleotide, may be the same, but each of the sense strand or antisense strand can be selected from several possibilities of modifications within the alternating motif such as “ABABAB . . . ”, “ACACAC . . . ” “BDBDBD . . . ” or “CDCDCD . . . ,” etc.

In one embodiment, the RNAi agent of the invention comprises the modification pattern for the alternating motif on the sense strand relative to the modification pattern for the alternating motif on the antisense strand is shifted. The shift may be such that the modified group of nucleotides of the sense strand corresponds to a differently modified group of nucleotides of the antisense strand and vice versa. For example, the sense strand when paired with the antisense strand in the dsRNA duplex, the alternating motif in the sense strand may start with “ABABAB” from 5′-3′ of the strand and the alternating motif in the antisense strand may start with “BABABA” from 5′-3′ of the strand within the duplex region. As another example, the alternating motif in the sense strand may start with “AABBAABB” from 5′-3′ of the strand and the alternating motif in the antisense strand may start with “BBAABBAA” from 5′-3′ of the strand within the duplex region, so that there is a complete or partial shift of the modification patterns between the sense strand and the antisense strand.

In one embodiment, the RNAi agent comprises the pattern of the alternating motif of 2′-O-methyl modification and 2′-F modification on the sense strand initially has a shift relative to the pattern of the alternating motif of 2′-O-methyl modification and 2′-F modification on the antisense strand initially, i.e., the 2′-O-methyl modified nucleotide on the sense strand base pairs with a 2′-F modified nucleotide on the antisense strand and vice versa. The 1 position of the sense strand may start with the 2′-F modification, and the 1 position of the antisense strand may start with the 2′-O-methyl modification.

The introduction of one or more motifs of three identical modifications on three consecutive nucleotides to the sense strand and/or antisense strand interrupts the initial modification pattern present in the sense strand and/or antisense strand. This interruption of the modification pattern of the sense and/or antisense strand by introducing one or more motifs of three identical modifications on three consecutive nucleotides to the sense and/or antisense strand surprisingly enhances the gene silencing activity to the target gene.

In one embodiment, when the motif of three identical modifications on three consecutive nucleotides is introduced to any of the strands, the modification of the nucleotide next to the motif is a different modification than the modification of the motif. For example, the portion of the sequence containing the motif is “ . . . N_(a)YYYN_(b) . . . ,” where “Y” represents the modification of the motif of three identical modifications on three consecutive nucleotide, and “N_(a)” and “N_(b)” represent a modification to the nucleotide next to the motif “YYY” that is different than the modification of Y, and where N_(a) and N_(b) can be the same or different modifications. Alternatively, N_(a) and/or N_(b) may be present or absent when there is a wing modification present.

The RNAi agent may further comprise at least one phosphorothioate or methylphosphonate internucleotide linkage. The phosphorothioate or methylphosphonate internucleotide linkage modification may occur on any nucleotide of the sense strand or antisense strand or both strands in any position of the strand. For instance, the internucleotide linkage modification may occur on every nucleotide on the sense strand and/or antisense strand; each internucleotide linkage modification may occur in an alternating pattern on the sense strand and/or antisense strand; or the sense strand or antisense strand may contain both internucleotide linkage modifications in an alternating pattern. The alternating pattern of the internucleotide linkage modification on the sense strand may be the same or different from the antisense strand, and the alternating pattern of the internucleotide linkage modification on the sense strand may have a shift relative to the alternating pattern of the internucleotide linkage modification on the antisense strand.

In one embodiment, the RNAi comprises a phosphorothioate or methylphosphonate internucleotide linkage modification in the overhang region. For example, the overhang region may contain two nucleotides having a phosphorothioate or methylphosphonate internucleotide linkage between the two nucleotides. Internucleotide linkage modifications also may be made to link the overhang nucleotides with the terminal paired nucleotides within the duplex region. For example, at least 2, 3, 4, or all the overhang nucleotides may be linked through phosphorothioate or methylphosphonate internucleotide linkage, and optionally, there may be additional phosphorothioate or methylphosphonate internucleotide linkages linking the overhang nucleotide with a paired nucleotide that is next to the overhang nucleotide. For instance, there may be at least two phosphorothioate internucleotide linkages between the terminal three nucleotides, in which two of the three nucleotides are overhang nucleotides, and the third is a paired nucleotide next to the overhang nucleotide. These terminal three nucleotides may be at the 3′-end of the antisense strand, the 3′-end of the sense strand, the 5′-end of the antisense strand, and/or the 5′end of the antisense strand.

In one embodiment, the 2 nucleotide overhang is at the 3′-end of the antisense strand, and there are two phosphorothioate internucleotide linkages between the terminal three nucleotides, wherein two of the three nucleotides are the overhang nucleotides, and the third nucleotide is a paired nucleotide next to the overhang nucleotide. Optionally, the RNAi agent may additionally have two phosphorothioate internucleotide linkages between the terminal three nucleotides at both the 5′-end of the sense strand and at the 5′-end of the antisense strand.

In one embodiment, the RNAi agent comprises mismatch(es) with the target, within the duplex, or combinations thereof. The mismatch may occur in the overhang region or the duplex region. The base pair may be ranked on the basis of their propensity to promote dissociation or melting (e.g., on the free energy of association or dissociation of a particular pairing, the simplest approach is to examine the pairs on an individual pair basis, though next neighbor or similar analysis can also be used). In terms of promoting dissociation: A:U is preferred over G:C; G:U is preferred over G:C; and I:C is preferred over G:C (I=inosine). Mismatches, e.g., non-canonical or other than canonical pairings (as described elsewhere herein) are preferred over canonical (A:T, A:U, G:C) pairings; and pairings which include a universal base are preferred over canonical pairings.

In one embodiment, the RNAi agent comprises at least one of the first 1, 2, 3, 4, or 5 base pairs within the duplex regions from the 5′-end of the antisense strand independently selected from the group of: A:U, G:U, I:C, and mismatched pairs, e.g., non-canonical or other than canonical pairings or pairings which include a universal base, to promote the dissociation of the antisense strand at the 5′-end of the duplex.

In one embodiment, the nucleotide at the 1 position within the duplex region from the 5′-end in the antisense strand is selected from the group consisting of A, dA, dU, U, and dT. Alternatively, at least one of the first 1, 2 or 3 base pair within the duplex region from the 5′-end of the antisense strand is an AU base pair. For example, the first base pair within the duplex region from the 5′-end of the antisense strand is an AU base pair.

In one embodiment, the sense strand sequence may be represented by formula (I):

5′ n_(p)-N_(a)-(X X X)_(i)-N_(b)-Y Y Y-N_(b)-(Z Z Z)_(j)-N_(a)-n_(q) 3′ (I)

wherein:

i and j are each independently 0 or 1;

p and q are each independently 0-6;

each N_(a) independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;

each N_(b) independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;

each n_(p) and n_(q) independently represent an overhang nucleotide;

wherein Nb and Y do not have the same modification; and

XXX, YYY and ZZZ each independently represent one motif of three identical modifications on three consecutive nucleotides. Preferably YYY is all 2′-F modified nucleotides.

In one embodiment, the N_(a) and/or N_(b) comprise modifications of alternating pattern.

In one embodiment, the YYY motif occurs at or near the cleavage site of the sense strand. For example, when the RNAi agent has a duplex region of 17-23 nucleotides in length, the YYY motif can occur at or the vicinity of the cleavage site (e.g.: can occur at positions 6, 7, 8, 7, 8, 9, 8, 9, 10, 9, 10, 11, 10, 11, 12 or 11, 12, 13) of—the sense strand, the count starting from the 1^(st) nucleotide, from the 5′-end; or optionally, the count starting at the 1^(st) paired nucleotide within the duplex region, from the 5′-end.

In one embodiment, i is 1 and j is 0, or i is 0 and j is 1, or both i and j are 1. The sense strand can therefore be represented b the following formulas:

5′ n_(p)-N_(a)-YYY-N_(b)-ZZZ-N_(a)-n_(q) 3′ (Ib); 5′ n_(p)-N_(a)-XXX-N_(b)-YYY-N_(a)-n_(q) 3′ (Ic);  or 5′ n_(p)-N_(a)-XXX-N_(b)-YYY-N_(b)-ZZZ-N_(a)-n_(q) 3′ (Id).

When the sense strand is represented by formula (Ib), N_(b) represents an oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a) independently can represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

When the sense strand is represented as formula (Ic), N_(b) represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a) can independently represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

When the sense strand is represented as formula (Id), each N_(b) independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Preferably, N_(b) is 0, 1, 2, 3, 4, 5 or 6 Each N_(a) can independently represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

Each of X, Y and Z may be the same or different from each other.

In other embodiments, i is 0 and j is 0, and the sense strand may be represented by the formula:

5′ n_(p)-N_(a)-YYY-N_(a)-n_(q) 3′ (Ia).

When the sense strand is represented by formula (Ia), each N_(a) independently can represent an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

In one embodiment, the antisense strand sequence of the RNAi may be represented by formula (II):

5′ n_(q)′-N_(a)′-(Z′Z′Z′)_(k)-N_(b)′-Y′Y′Y′-N_(b)′-(X′X′X′)_(l)- N_(a)′-n_(p)′ 3′ (II)

wherein:

k and l are each independently 0 or 1;

p′ and q′ are each independently 0-6;

each N_(a)′ independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides;

each N_(b)′ independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;

each n_(p)′ and n_(q)′ independently represent an overhang nucleotide;

wherein N_(b)′ and Y′ do not have the same modification;

and

X′X′X′, Y′Y′Y′ and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides.

In one embodiment, the N_(a)′ and/or N_(b)′ comprise modifications of alternating pattern.

The Y′Y′Y′ motif occurs at or near the cleavage site of the antisense strand. For example, when the RNAi agent has a duplex region of 17-23 nucleotide in length, the Y′Y′Y′ motif can occur at positions 9, 10, 11; 10, 11, 12; 11, 12, 13; 12, 13, 14; or 13, 14, 15 of the antisense strand, with the count starting from the 1^(st) nucleotide, from the 5′-end; or optionally, the count starting at the 1^(st) paired nucleotide within the duplex region, from the 5′-end. Preferably, the Y′Y′Y′ motif occurs at positions 11, 12, 13.

In one embodiment, Y′Y′Y′ motif is all 2′-OMe modified nucleotides.

In one embodiment, k is 1 and 1 is 0, or k is 0 and 1 is 1, or both k and l are 1.

The antisense strand can therefore be represented by the following formulas:

5′ n_(q)′-N_(a)′-Z′Z′Z′-N_(b)′-Y′Y′Y′-N_(a)′-n_(p)′ 3′ (IIb); 5′ n_(q)′-N_(a)′-Y′Y′Y′-N_(b)′-X′X′X′-n_(p)′ 3′  (IIc);  or 5′ n_(q)′-N_(a)′-Z′Z′Z′-N_(b)′-Y′Y′Y′-N_(b)′-X′X′X′-N_(a)′-n_(p)′ 3′  (IId).

When the antisense strand is represented by formula (IIb), N_(b)′ represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a)′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

When the antisense strand is represented as formula (IIc), N_(b)′ represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a)′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

When the antisense strand is represented as formula (IId), each N_(b)′ independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides.

Each N_(a)′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides. Preferably, N_(b) is 0, 1, 2, 3, 4, 5 or 6.

In other embodiments, k is 0 and 1 is 0 and the antisense strand may be represented by the formula:

5′ n_(p)′-N_(a)′-Y′Y′Y′-N_(a)′-n_(q)′ 3′ (Ia).

When the antisense strand is represented as formula (IIa), each N_(a)′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

Each of X′, Y′ and Z′ may be the same or different from each other.

Each nucleotide of the sense strand and antisense strand may be independently modified with LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O-methyl, 2′-O-allyl, 2′-C-allyl, 2′-hydroxyl, or 2′-fluoro. For example, each nucleotide of the sense strand and antisense strand is independently modified with 2′-O-methyl or 2′-fluoro. Each X, Y, Z, X′, Y′ and Z′, in particular, may represent a 2′-O-methyl modification or a 2′-fluoro modification.

In one embodiment, the sense strand of the RNAi agent may contain YYY motif occurring at 9, 10 and 11 positions of the strand when the duplex region is 21 nt, the count starting from the 1^(st) nucleotide from the 5′-end, or optionally, the count starting at the 1^(st) paired nucleotide within the duplex region, from the 5′-end; and Y represents 2′-F modification. The sense strand may additionally contain XXX motif or ZZZ motifs as wing modifications at the opposite end of the duplex region; and XXX and ZZZ each independently represents a 2′-OMe modification or 2′-F modification.

In one embodiment the antisense strand may contain Y′Y′Y′ motif occurring at positions 11, 12, 13 of the strand, the count starting from the 1^(st) nucleotide from the 5′-end, or optionally, the count starting at the 1^(st) paired nucleotide within the duplex region, from the 5′-end; and Y′ represents 2′-O-methyl modification. The antisense strand may additionally contain X′X′X′ motif or Z′Z′Z′ motifs as wing modifications at the opposite end of the duplex region; and X′X′X′ and Z′Z′Z′ each independently represents a 2′-OMe modification or 2′-F modification.

The sense strand represented by any one of the above formulas (Ia), (Ib), (Ic), and (Id) forms a duplex with an antisense strand being represented by any one of formulas (IIa), (IIb), (IIc), and (IId), respectively.

Accordingly, the RNAi agents for use in the methods of the invention may comprise a sense strand and an antisense strand, each strand having 14 to 30 nucleotides, the RNAi duplex represented by formula (III):

sense: 5′ n_(p)-N_(a)-(X X X)_(i)-N_(b)-Y Y Y-N_(b)-(Z Z Z)_(j)-N_(a)-n_(q) 3′ antisense: 3′ n_(p)′-N_(a)′-(X′X′X′)_(k)-N_(b)′-Y′Y′Y′-N_(b)′-(Z′Z′Z′)_(l)- N_(a)′-n_(q)′ 5′ (III)

wherein:

i, j, k, and 1 are each independently 0 or 1;

p, p′, q, and q′ are each independently 0-6;

each N_(a) and N_(a)′ independently represents an oligonucleotide sequence comprising 0-25 modified nucleotides, each sequence comprising at least two differently modified nucleotides; each N_(b) and N_(b)′ independently represents an oligonucleotide sequence comprising 0-10 modified nucleotides;

wherein

each np′, n_(p), n_(q)′, and n_(q), each of which may or may not be present, independently represents an overhang nucleotide; and

XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides.

In one embodiment, i is 0 and j is 0; or i is 1 and j is 0; or i is 0 and j is 1; or both i and j are 0; or both i and j are 1. In another embodiment, k is 0 and 1 is 0; or k is 1 and 1 is 0; k is 0 and 1 is 1; or both k and l are 0; or both k and l are 1.

Exemplary combinations of the sense strand and antisense strand forming a RNAi duplex include the formulas below:

5′ n_(p)-N_(a)-Y Y Y-N_(a)-n_(q) 3′ 3′ n_(p)′-N_(a)′-Y′Y′Y′-N_(a)′n_(q)′ 5′ (IIIa) 5′ n_(p)-N_(a)-Y Y Y-N_(b)-Z Z Z-N_(a)-n_(q) 3′ 3′ n_(p)′-N_(a)′-Y′Y′Y′-N_(b)′-Z′Z′Z′-N_(a)′n_(q)′ 5′ (IIIb) 5′ n_(p)-N_(a)-X X X-N_(b)-Y Y Y-N_(a)-n_(q) 3′ 3′ n_(p)′-N_(a)′-X′X′X′-N_(b)′-Y′Y′Y′-N_(a)′-n_(q)′ 5′ (IIIc) 5′ n_(p)-N_(a)-X X X-N_(b)-Y Y Y-N_(b)-Z Z Z-N_(a)-n_(q) 3′ 3′ n_(p)′-N_(a)′-X′X′X′-N_(b)′-Y′Y′Y′-N_(b)′-Z′Z′Z′-N_(a)-n_(q)′ 5′ (IIId)

When the RNAi agent is represented by formula (IIIa), each N_(a) independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

When the RNAi agent is represented by formula (IIIb), each N_(b) independently represents an oligonucleotide sequence comprising 1-10, 1-7, 1-5 or 1-4 modified nucleotides. Each N_(a) independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

When the RNAi agent is represented as formula (IIIc), each N_(b), N_(b)′ independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a) independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.

When the RNAi agent is represented as formula (IIId), each N_(b), N_(b)′ independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a), N_(a)′ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides. Each of N_(a), N_(a)′, N_(b) and N_(b)′ independently comprises modifications of alternating pattern.

Each of X, Y and Z in formulas (III), (IIIa), (IIIb), (IIc), and (IIId) may be the same or different from each other.

When the RNAi agent is represented by formula (III), (IIIa), (IIIb), (IIc), and (IIId), at least one of the Y nucleotides may form a base pair with one of the Y′ nucleotides. Alternatively, at least two of the Y nucleotides form base pairs with the corresponding Y′ nucleotides; or all three of the Y nucleotides all form base pairs with the corresponding Y′ nucleotides.

When the RNAi agent is represented by formula (IIIb) or (IIId), at least one of the Z nucleotides may form a base pair with one of the Z′ nucleotides. Alternatively, at least two of the Z nucleotides form base pairs with the corresponding Z′ nucleotides; or all three of the Z nucleotides all form base pairs with the corresponding Z′ nucleotides.

When the RNAi agent is represented as formula (IIIc) or (IIId), at least one of the X nucleotides may form a base pair with one of the X′ nucleotides. Alternatively, at least two of the X nucleotides form base pairs with the corresponding X′ nucleotides; or all three of the X nucleotides all form base pairs with the corresponding X′ nucleotides.

In one embodiment, the modification on the Y nucleotide is different than the modification on the Y′ nucleotide, the modification on the Z nucleotide is different than the modification on the Z′ nucleotide, and/or the modification on the X nucleotide is different than the modification on the X′ nucleotide.

In one embodiment, when the RNAi agent is represented by formula (IIId), the N_(a) modifications are 2′-O-methyl or 2′-fluoro modifications. In another embodiment, when the RNAi agent is represented by formula (IIId), the N_(a) modifications are 2′-O-methyl or 2′-fluoro modifications and n_(p)′>0 and at least one n_(p)′ is linked to a neighboring nucleotide a via phosphorothioate linkage. In yet another embodiment, when the RNAi agent is represented by formula (IIId), the N_(a) modifications are 2′-O-methyl or 2′-fluoro modifications, n_(p)′>0 and at least one n_(p)′ is linked to a neighboring nucleotide via phosphorothioate linkage, and the sense strand is conjugated to one or more GalNAc derivatives attached through a bivalent or trivalent branched linker. In another embodiment, when the RNAi agent is represented by formula (IIId), the N_(a) modifications are 2′-O-methyl or 2′-fluoro modifications, n_(p)′>0 and at least one n_(p)′ is linked to a neighboring nucleotide via phosphorothioate linkage, the sense strand comprises at least one phosphorothioate linkage, and the sense strand is conjugated to one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.

In one embodiment, when the RNAi agent is represented by formula (IIIa), the N_(a) modifications are 2′-O-methyl or 2′-fluoro modifications, n_(p)′>0 and at least one n_(p)′ is linked to a neighboring nucleotide via phosphorothioate linkage, the sense strand comprises at least one phosphorothioate linkage, and the sense strand is conjugated to one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.

In one embodiment, the RNAi agent is a multimer containing at least two duplexes represented by formula (III), (IIIa), (IIIb), (IIc), and (IIId), wherein the duplexes are connected by a linker. The linker can be cleavable or non-cleavable. Optionally, the multimer further comprises a ligand. Each of the duplexes can target the same gene or two different genes; or each of the duplexes can target same gene at two different target sites.

In one embodiment, the RNAi agent is a multimer containing three, four, five, six or more duplexes represented by formula (III), (IIIa), (IIIb), (IIc), and (IIId), wherein the duplexes are connected by a linker. The linker can be cleavable or non-cleavable. Optionally, the multimer further comprises a ligand. Each of the duplexes can target the same gene or two different genes; or each of the duplexes can target same gene at two different target sites.

In one embodiment, two RNAi agents represented by formula (III), (IIIa), (IIIb), (IIc), and (IIId) are linked to each other at the 5′ end, and one or both of the 3′ ends and are optionally conjugated to a ligand. Each of the agents can target the same gene or two different genes; or each of the agents can target same gene at two different target sites.

Various publications describe multimeric RNAi agents that can be used in the methods of the invention. Such publications include WO2007/091269, U.S. Pat. No. 7,858,769, WO2010/141511, WO2007/117686, WO2009/014887 and WO2011/031520 the entire contents of each of which are hereby incorporated herein by reference.

The RNAi agent that contains conjugations of one or more carbohydrate moieties to a RNAi agent can optimize one or more properties of the RNAi agent. In many cases, the carbohydrate moiety will be attached to a modified subunit of the RNAi agent. For example, the ribose sugar of one or more ribonucleotide subunits of a dsRNA agent can be replaced with another moiety, e.g., a non-carbohydrate (preferably cyclic) carrier to which is attached a carbohydrate ligand. A ribonucleotide subunit in which the ribose sugar of the subunit has been so replaced is referred to herein as a ribose replacement modification subunit (RRMS). A cyclic carrier may be a carbocyclic ring system, i.e., all ring atoms are carbon atoms, or a heterocyclic ring system, i.e., one or more ring atoms may be a heteroatom, e.g., nitrogen, oxygen, sulfur. The cyclic carrier may be a monocyclic ring system, or may contain two or more rings, e.g. fused rings. The cyclic carrier may be a fully saturated ring system, or it may contain one or more double bonds.

The ligand may be attached to the polynucleotide via a carrier. The carriers include (i) at least one “backbone attachment point,” preferably two “backbone attachment points” and (ii) at least one “tethering attachment point.” A “backbone attachment point” as used herein refers to a functional group, e.g. a hydroxyl group, or generally, a bond available for, and that is suitable for incorporation of the carrier into the backbone, e.g., the phosphate, or modified phosphate, e.g., sulfur containing, backbone, of a ribonucleic acid. A “tethering attachment point” (TAP) in some embodiments refers to a constituent ring atom of the cyclic carrier, e.g., a carbon atom or a heteroatom (distinct from an atom which provides a backbone attachment point), that connects a selected moiety. The moiety can be, e.g., a carbohydrate, e.g. monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide and polysaccharide. Optionally, the selected moiety is connected by an intervening tether to the cyclic carrier. Thus, the cyclic carrier will often include a functional group, e.g., an amino group, or generally, provide a bond, that is suitable for incorporation or tethering of another chemical entity, e.g., a ligand to the constituent ring.

The RNAi agents may be conjugated to a ligand via a carrier, wherein the carrier can be cyclic group or acyclic group; preferably, the cyclic group is selected from pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolane, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl and decalin; preferably, the acyclic group is selected from serinol backbone or diethanolamine backbone.

In certain specific embodiments, the RNAi agent for use in the methods of the invention is an agent selected from the group of agents listed in any one of Tables 1a, Ib, 2a, 2b, 2c, 10-13, and 15. In one embodiment, when the agent is an agent listed in Table 1, the agent may lack a terminal dT.

The present invention further includes double-stranded RNAi agents comprising any one of the sequences listed in any one of Tables 1 or 2 which comprise a 5′ phosphate or phosphate mimetic on the antisense strand (see, e.g., PCT Publication No. WO 2011005860). Further, the present invention includes double-stranded RNAi agents comprising any one of the sequences listed in any one of Tables 1a, Ib, 2a, 2b, 2c, 10-13, and 15 which include a 2′fluoro group in place of a 2′-OMe group at the 5′end of the sense strand.

B. Additional Motifs

In certain aspects, the double-stranded RNAi agents described herein comprises a sense strand and an antisense strand wherein said sense strand and an antisense strand comprise less than eleven, ten, nine, eight, seven, six, or five 2′-deoxyflouro.

In certain aspects, the double-stranded RNAi agents described herein comprises a sense strand and an antisense strand, wherein said sense strand and an antisense strand comprise less than ten, nine, eight, seven, six, five, four phosphorothioate internucleotide linkages.

In certain aspects, the double-stranded RNAi agents described herein comprises a sense strand and an antisense strand, wherein said sense strand and an antisense strand comprise less than ten 2′-deoxyflouro and less than six phosphorothioate internucleotide linkages.

In certain aspects, the double-stranded RNAi agents described herein comprises a sense strand and an antisense strand, wherein said sense strand and an antisense strand comprise less than eight 2′-deoxyflouro and less than six phosphorothioate internucleotide linkages.

In certain aspects, the double-stranded RNAi agents described herein comprises a sense strand and an antisense strand, wherein said sense strand and an antisense strand comprise less than nine 2′-deoxyflouro and less than six phosphorothioate internucleotide linkages.

Double stranded RNAi agent suitable for use in the methods of the present invention are also provided in U.S. Pat. No. 10,478,500, the entire contents of which is incorporated herein by reference.

V. Ligands

The double-stranded RNAi agents of the invention may optionally be conjugated to one or more ligands. The ligand can be attached to the sense strand, antisense strand or both strands, at the 3′-end, 5′-end or both ends. For instance, the ligand may be conjugated to the sense strand. In some embodiments, the ligand is conjugated to the 3′-end of the sense strand. In one embodiment, the ligand is a GalNAc ligand. In particularly some embodiments, the ligand is GalNAc₃. The ligands are coupled, preferably covalently, either directly or indirectly via an intervening tether.

In some embodiments, a ligand alters the distribution, targeting or lifetime of the molecule into which it is incorporated. In some embodiments a ligand provides an enhanced affinity for a selected target, e.g., molecule, cell or cell type, compartment, receptor e.g., a cellular or organ compartment, tissue, organ or region of the body, as, e.g., compared to a species absent such a ligand. Ligands providing enhanced affinity for a selected target are also termed targeting ligands.

Some ligands can have endosomolytic properties. The endosomolytic ligands promote the lysis of the endosome and/or transport of the composition of the invention, or its components, from the endosome to the cytoplasm of the cell. The endosomolytic ligand may be a polyanionic peptide or peptidomimetic which shows pH-dependent membrane activity and fusogenicity. In one embodiment, the endosomolytic ligand assumes its active conformation at endosomal pH. The “active” conformation is that conformation in which the endosomolytic ligand promotes lysis of the endosome and/or transport of the composition of the invention, or its components, from the endosome to the cytoplasm of the cell. Exemplary endosomolytic ligands include the GALA peptide (Subbarao et al., Biochemistry, 1987, 26: 2964-2972), the EALA peptide (Vogel et al., J. Am. Chem. Soc., 1996, 118: 1581-1586), and their derivatives (Turk et al., Biochem. Biophys. Acta, 2002, 1559: 56-68). In one embodiment, the endosomolytic component may contain a chemical group (e.g., an amino acid) which will undergo a change in charge or protonation in response to a change in pH. The endosomolytic component may be linear or branched.

Ligands can improve transport, hybridization, and specificity properties and may also improve nuclease resistance of the resultant natural or modified oligoribonucleotide, or a polymeric molecule comprising any combination of monomers described herein and/or natural or modified ribonucleotides.

Ligands in general can include therapeutic modifiers, e.g., for enhancing uptake; diagnostic compounds or reporter groups e.g., for monitoring distribution; cross-linking agents; and nuclease-resistance conferring moieties. General examples include lipids, steroids, vitamins, sugars, proteins, peptides, polyamines, and peptide mimics.

Ligands can include a naturally occurring substance, such as a protein (e.g., human serum albumin (HSA), low-density lipoprotein (LDL), high-density lipoprotein (HDL), or globulin); a carbohydrate (e.g., a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin or hyaluronic acid); or a lipid. The ligand may also be a recombinant or synthetic molecule, such as a synthetic polymer, e.g., a synthetic polyamino acid, an oligonucleotide (e.g., an aptamer). Examples of polyamino acids include polyamino acid is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolied) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacryllic acid), N-isopropylacrylamide polymers, or polyphosphazine. Example of polyamines include: polyethylenimine, polylysine (PLL), spermine, spermidine, polyamine, pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, arginine, amidine, protamine, cationic lipid, cationic porphyrin, quaternary salt of a polyamine, or an alpha helical peptide.

Ligands can also include targeting groups, e.g., a cell or tissue targeting agent, e.g., a lectin, glycoprotein, lipid or protein, e.g., an antibody, that binds to a specified cell type such as a kidney cell. A targeting group can be a thyrotropin, melanotropin, lectin, glycoprotein, surfactant protein A, Mucin carbohydrate, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, multivalent fucose, glycosylated polyaminoacids, multivalent galactose, transferrin, bisphosphonate, polyglutamate, polyaspartate, a lipid, cholesterol, a steroid, bile acid, folate, vitamin B12, biotin, an RGD peptide, an RGD peptide mimetic or an aptamer.

Other examples of ligands include dyes, intercalating agents (e.g., acridines), cross-linkers (e.g., psoralene, mitomycin C), porphyrins (TPPC4, texaphyrin, Sapphyrin), polycyclic aromatic hydrocarbons (e.g., phenazine, dihydrophenazine), artificial endonucleases or a chelator (e.g., EDTA), lipophilic molecules, e.g., cholesterol, cholic acid, adamantane acetic acid, 1-pyrene butyric acid, dihydrotestosterone, 1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid, myristic acid,O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine) and peptide conjugates (e.g., antennapedia peptide, Tat peptide), alkylating agents, phosphate, amino, mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG]₂, polyamino, alkyl, substituted alkyl, radiolabeled markers, enzymes, haptens (e.g., biotin), transport/absorption facilitators (e.g., aspirin, vitamin E, folic acid), synthetic ribonucleases (e.g., imidazole, bisimidazole, histamine, imidazole clusters, acridine-imidazole conjugates, Eu3+ complexes of tetraazamacrocycles), dinitrophenyl, HRP, or AP.

Ligands can be proteins, e.g., glycoproteins, or peptides, e.g., molecules having a specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell. Ligands may also include hormones and hormone receptors. They can also include non-peptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, multivalent fucose, or aptamers. The ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF-κB.

The ligand can be a substance, e.g., a drug, which can increase the uptake of the iRNA agent into the cell, for example, by disrupting the cell's cytoskeleton, e.g., by disrupting the cell's microtubules, microfilaments, and/or intermediate filaments. The drug can be, for example, taxon, vincristine, vinblastine, cytochalasin, nocodazole, japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.

The ligand can increase the uptake of the oligonucleotide into the cell by, for example, activating an inflammatory response. Exemplary ligands that would have such an effect include tumor necrosis factor alpha (TNFalpha), interleukin-1 beta, or gamma interferon.

In one aspect, the ligand is a lipid or lipid-based molecule. Such a lipid or lipid-based molecule preferably binds a serum protein, e.g., human serum albumin (HSA). An HSA binding ligand allows for distribution of the conjugate to a target tissue, e.g., a non-kidney target tissue of the body. For example, the target tissue can be the liver, including parenchymal cells of the liver. Other molecules that can bind HSA can also be used as ligands. For example, naproxen or aspirin can be used. A lipid or lipid-based ligand can (a) increase resistance to degradation of the conjugate, (b) increase targeting or transport into a target cell or cell membrane, and/or (c) can be used to adjust binding to a serum protein, e.g., HSA.

A lipid based ligand can be used to modulate, e.g., control the binding of the conjugate to a target tissue. For example, a lipid or lipid-based ligand that binds to HSA more strongly will be less likely to be targeted to the kidney and therefore less likely to be cleared from the body. A lipid or lipid-based ligand that binds to HSA less strongly can be used to target the conjugate to the kidney.

In one embodiment, the lipid based ligand binds HSA. Preferably, it binds HSA with a sufficient affinity such that the conjugate will be preferably distributed to a non-kidney tissue. In one embodiment, the affinity is such that that the HSA-ligand binding can be reversed. In another embodiment, the lipid based ligand binds HSA weakly or not at all, such that the conjugate will be preferably distributed to the kidney. Other moieties that target to kidney cells can also be used in place of or in addition to the lipid based ligand.

In another aspect, the ligand is a moiety, e.g., a vitamin, which is taken up by a target cell, e.g., a proliferating cell. These are particularly useful for treating disorders characterized by unwanted cell proliferation, e.g., of the malignant or non-malignant type, e.g., cancer cells. Exemplary vitamins include vitamin A, E, and K. Other exemplary vitamins include B vitamins, e.g., folic acid, B12, riboflavin, biotin, pyridoxal or other vitamins or nutrients taken up by cancer cells. Also included are HAS, low density lipoprotein (LDL) and high-density lipoprotein (HDL).

In another aspect, the ligand is a cell-permeation agent, preferably a helical cell-permeation agent. Preferably, the agent is amphipathic. An exemplary agent is a peptide such as tat or antennopedia. If the agent is a peptide, it can be modified, including a peptidylmimetic, invertomers, non-peptide or pseudo-peptide linkages, and use of D-amino acids. The helical agent is preferably an alpha-helical agent, which preferably has a lipophilic and a lipophobic phase.

The ligand can be a peptide or peptidomimetic. A peptidomimetic (also referred to herein as an oligopeptidomimetic) is a molecule capable of folding into a defined three-dimensional structure similar to a natural peptide. The peptide or peptidomimetic moiety can be about 5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long. A peptide or peptidomimetic can be, for example, a cell permeation peptide, cationic peptide, amphipathic peptide, or hydrophobic peptide (e.g., consisting primarily of Tyr, Trp or Phe). The peptide moiety can be a dendrimer peptide, constrained peptide or crosslinked peptide. In another alternative, the peptide moiety can include a hydrophobic membrane translocation sequence (MTS). An exemplary hydrophobic MTS-containing peptide is RFGF having the amino acid sequence AAVALLPAVLLALLAP (SEQ ID NO: 3). An RFGF analogue (e.g., amino acid sequence AALLPVLLAAP (SEQ ID NO: 4)) containing a hydrophobic MTS can also be a targeting moiety. The peptide moiety can be a “delivery” peptide, which can carry large polar molecules including peptides, oligonucleotides, and protein across cell membranes. For example, sequences from the HIV Tat protein (GRKKRRQRRRPPQ) (SEQ ID NO: 5) and the Drosophila Antennapedia protein (RQIKIWFQNRRMKWKK) (SEQ ID NO: 6) have been found to be capable of functioning as delivery peptides. A peptide or peptidomimetic can be encoded by a random sequence of DNA, such as a peptide identified from a phage-display library, or one-bead-one-compound (OBOC) combinatorial library (Lam et al., Nature, 354:82-84, 1991). Preferably the peptide or peptidomimetic tethered to an iRNA agent via an incorporated monomer unit is a cell targeting peptide such as an arginine-glycine-aspartic acid (RGD)-peptide, or RGD mimic. A peptide moiety can range in length from about 5 amino acids to about 40 amino acids. The peptide moieties can have a structural modification, such as to increase stability or direct conformational properties. Any of the structural modifications described below can be utilized. An RGD peptide moiety can be used to target a tumor cell, such as an endothelial tumor cell or a breast cancer tumor cell (Zitzmann et al., Cancer Res., 62:5139-43, 2002). An RGD peptide can facilitate targeting of an iRNA agent to tumors of a variety of other tissues, including the lung, kidney, spleen, or liver (Aoki et al., Cancer Gene Therapy 8:783-787, 2001). Preferably, the RGD peptide will facilitate targeting of an iRNA agent to the kidney. The RGD peptide can be linear or cyclic, and can be modified, e.g., glycosylated or methylated to facilitate targeting to specific tissues. For example, a glycosylated RGD peptide can deliver an iRNA agent to a tumor cell expressing αvß₃ (Haubner et al., Jour. Nucl. Med., 42:326-336, 2001). Peptides that target markers enriched in proliferating cells can be used. For example, RGD containing peptides and peptidomimetics can target cancer cells, in particular cells that exhibit an integrin. Thus, one could use RGD peptides, cyclic peptides containing RGD, RGD peptides that include D-amino acids, as well as synthetic RGD mimics. In addition to RGD, one can use other moieties that target the integrin ligand. Generally, such ligands can be used to control proliferating cells and angiogenesis. Some conjugates of this type of ligand target PECAM-1, VEGF, or other cancer gene, e.g., a cancer gene described herein.

A “cell permeation peptide” is capable of permeating a cell, e.g., a microbial cell, such as a bacterial or fungal cell, or a mammalian cell, such as a human cell. A microbial cell-permeating peptide can be, for example, an α-helical linear peptide (e.g., LL-37 or Ceropin P1), a disulfide bond-containing peptide (e.g., α-defensin, β-defensin or bactenecin), or a peptide containing only one or two dominating amino acids (e.g., PR-39 or indolicidin). A cell permeation peptide can also include a nuclear localization signal (NLS). For example, a cell permeation peptide can be a bipartite amphipathic peptide, such as MPG, which is derived from the fusion peptide domain of HIV-1 gp41 and the NLS of SV40 large T antigen (Simeoni et al., Nucl. Acids Res. 31:2717-2724, 2003).

In one embodiment, a targeting peptide can be an amphipathic α-helical peptide. Exemplary amphipathic α-helical peptides include, but are not limited to, cecropins, lycotoxins, paradaxins, buforin, CPF, bombinin-like peptide (BLP), cathelicidins, ceratotoxins, S. clava peptides, hagfish intestinal antimicrobial peptides (HFIAPs), magainines, brevinins-2, dermaseptins, melittins, pleurocidin, H2A peptides, Xenopus peptides, esculentinis-1, and caerins. A number of factors will preferably be considered to maintain the integrity of helix stability. For example, a maximum number of helix stabilization residues will be utilized (e.g., leu, ala, or lys), and a minimum number helix destabilization residues will be utilized (e.g., proline, or cyclic monomeric units. The capping residue will be considered (for example Gly is an exemplary N-capping residue and/or C-terminal amidation can be used to provide an extra H-bond to stabilize the helix. Formation of salt bridges between residues with opposite charges, separated by i±3, or i±4 positions can provide stability. For example, cationic residues such as lysine, arginine, homo-arginine, ornithine or histidine can form salt bridges with the anionic residues glutamate or aspartate.

Peptide and peptidomimetic ligands include those having naturally occurring or modified peptides, e.g., D or L peptides; a, J, or y peptides; N-methyl peptides; azapeptides; peptides having one or more amide, i.e., peptide, linkages replaced with one or more urea, thiourea, carbamate, or sulfonyl urea linkages; or cyclic peptides.

The targeting ligand can be any ligand that is capable of targeting a specific receptor. Examples are: folate, GalNAc, galactose, mannose, mannose-6P, clusters of sugars such as GalNAc cluster, mannose cluster, galactose cluster, or an aptamer. A cluster is a combination of two or more sugar units. The targeting ligands also include integrin receptor ligands, Chemokine receptor ligands, transferrin, biotin, serotonin receptor ligands, PSMA, endothelin, GCPII, somatostatin, LDL and HDL ligands. The ligands can also be based on nucleic acid, e.g., an aptamer. The aptamer can be unmodified or have any combination of modifications disclosed herein.

Endosomal release agents include imidazoles, poly or oligoimidazoles, PEIs, peptides, fusogenic peptides, polycaboxylates, polyacations, masked oligo or poly cations or anions, acetals, polyacetals, ketals/polyketyals, orthoesters, polymers with masked or unmasked cationic or anionic charges, dendrimers with masked or unmasked cationic or anionic charges.

PK modulator stands for pharmacokinetic modulator. PK modulators include lipophiles, bile acids, steroids, phospholipid analogues, peptides, protein binding agents, PEG, vitamins etc.

Exemplary PK modulators include, but are not limited to, cholesterol, fatty acids, cholic acid, lithocholic acid, dialkylglycerides, diacylglyceride, phospholipids, sphingolipids, naproxen, ibuprofen, vitamin E, biotin etc. Oligonucleotides that comprise a number of phosphorothioate linkages are also known to bind to serum protein, thus short oligonucleotides, e.g., oligonucleotides of about 5 bases, 10 bases, 15 bases or 20 bases, comprising multiple phosphorothioate linkages in the backbone are also amenable to the present invention as ligands (e.g., as PK modulating ligands).

In addition, aptamers that bind serum components (e.g., serum proteins) are also amenable to the present invention as PK modulating ligands.

Other ligand conjugates amenable to the invention are described in U.S. patent application Ser. No. 10/916,185, filed Aug. 10, 2004; U.S. Ser. No. 10/946,873, filed Sep. 21, 2004; U.S. Ser. No. 10/833,934, filed Aug. 3, 2007; U.S. Ser. No. 11/115,989 filed Apr. 27, 2005 and U.S. Ser. No. 11/944,227 filed Nov. 21, 2007, which are incorporated by reference in their entireties for all purposes.

When two or more ligands are present, the ligands can all have same properties, all have different properties or some ligands have the same properties while others have different properties. For example, a ligand can have targeting properties, have endosomolytic activity or have PK modulating properties. In one embodiment, all the ligands have different properties.

Ligands can be coupled to the oligonucleotides at various places, for example, 3′-end, 5′-end, and/or at an internal position. In some embodiments, the ligand is attached to the oligonucleotides via an intervening tether, e.g., a carrier described herein. The ligand or tethered ligand may be present on a monomer when the monomer is incorporated into the growing strand. In some embodiments, the ligand may be incorporated via coupling to a “precursor” monomer after the “precursor” monomer has been incorporated into the growing strand. For example, a monomer having, e.g., an amino-terminated tether (i.e., having no associated ligand), e.g., TAP—(CH₂)·NH₂ may be incorporated into a growing oligonucleotides strand. In a subsequent operation, i.e., after incorporation of the precursor monomer into the strand, a ligand having an electrophilic group, e.g., a pentafluorophenyl ester or aldehyde group, can subsequently be attached to the precursor monomer by coupling the electrophilic group of the ligand with the terminal nucleophilic group of the precursor monomer's tether.

In another example, a monomer having a chemical group suitable for taking part in Click Chemistry reaction may be incorporated, e.g., an azide or alkyne terminated tether/linker. In a subsequent operation, i.e., after incorporation of the precursor monomer into the strand, a ligand having complementary chemical group, e.g. an alkyne or azide can be attached to the precursor monomer by coupling the alkyne and the azide together.

In some embodiments, a ligand can be conjugated to nucleobases, sugar moieties, or internucleosidic linkages of nucleic acid molecules. Conjugation to purine nucleobases or derivatives thereof can occur at any position including, endocyclic and exocyclic atoms. In some embodiments, the 2-, 6-, 7-, or 8-positions of a purine nucleobase are attached to a conjugate moiety. Conjugation to pyrimidine nucleobases or derivatives thereof can also occur at any position. In some embodiments, the 2-, 5-, and 6-positions of a pyrimidine nucleobase can be substituted with a conjugate moiety. Conjugation to sugar moieties of nucleosides can occur at any carbon atom. Example carbon atoms of a sugar moiety that can be attached to a conjugate moiety include the 2′, 3′, and 5′ carbon atoms. The 1′ position can also be attached to a conjugate moiety, such as in an abasic residue. Internucleosidic linkages can also bear conjugate moieties. For phosphorus-containing linkages (e.g., phosphodiester, phosphorothioate, phosphorodithiotate, phosphoroamidate, and the like), the conjugate moiety can be attached directly to the phosphorus atom or to an O, N, or S atom bound to the phosphorus atom. For amine- or amide-containing internucleosidic linkages (e.g., PNA), the conjugate moiety can be attached to the nitrogen atom of the amine or amide or to an adjacent carbon atom.

In some embodiment, an siRNA targeting an HAO1 gene is conjugated to a carbohydrate e.g. monosaccharide (such as GalNAc), disaccharide, trisaccharide, tetrasaccharide, polysaccharide. In some embodiments, the siRNA is conjugated to N-acetylgalactosamine (GalNAc) ligand. The enhances efficient delivery to hepatocytes following subcutaneous administration. Methods of conjugation of carbohydrates, e.g., N-acetylgalactosamine, to, e.g., an siRNA are well known to one of skill in the art. Examples can be found in U.S. Pat. No. 8,106,022 and WO2014/025805.

In some embodiments, an siRNA targeting an HAO1 gene is conjugated to a ligand, e.g., to GalNac, via a linker. For example, the ligand can be one or more GalNAc (N-acetylglucosamine) derivatives attached through a bivalent or trivalent branched linker.

In one embodiment, the dsRNA of the invention is conjugated to a bivalent and trivalent branched linkers include the structures shown in any of formula (IV)-(VII):

wherein:

q^(2A), q^(2B), q^(3A), q^(3B), q^(4A), q^(4B), q^(5A), q^(5B) and q^(5C) represent independently for each occurrence 0-20 and wherein the repeating unit can be the same or different;

P^(2A), P^(2B), P^(3A), P^(3B), P^(4A), P^(4B), P^(5A), P^(5B), P^(5C), T^(2A), T^(2B) T^(3A), T^(3B), T^(4A), T^(4B), T^(4A), T^(5B), T^(5C) are each independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O), CH₂, CH₂NH or CH₂O;

Q^(2A), Q^(2B), Q^(3A), Q^(3B), Q^(4A), Q^(4B), Q^(5A), Q^(5B), Q^(5C) are independently for each occurrence absent, alkylene, substituted alkylene wherein one or more methylenes can be interrupted or terminated by one or more of O, S, S(O), SO₂, N(R^(N)), C(R′)═C(R″), C≡C or C(O);

R^(2A), R^(2B), R^(3A), R^(3B), R^(4A), R^(4B), R^(5A), R^(5B), R^(5C) are each independently for each occurrence absent, NH, O, S, CH₂, C(O)O, C(O)NH, NHCH(R^(a))C(O), —C(O)—CH(R^(a))—NH—, CO, CH═N—O,

or heterocyclyl;

L^(2A), L^(2B), L^(3A), L^(3B), L^(4A), L^(4B), L^(5A), L^(5B) and L^(5C) represent the ligand; i.e. each independently for each occurrence a monosaccharide (such as GalNAc), disaccharide, trisaccharide, tetrasaccharide, oligosaccharide, or polysaccharide; and

R^(a) is H or amino acid side chain.

-   -   Trivalent conjugating GalNAc derivatives are particularly useful         for use with RNAi agents for inhibiting the expression of a         target gene, such as those of formula (VII):

wherein L^(5A), L^(5B) and L^(5C) represent a monosaccharide, such as GalNAc derivative.

Examples of suitable bivalent and trivalent branched linker groups conjugating GalNAc derivatives include, but are not limited to, the following compounds:

In some embodiments the ligand is selected from one of the following:

VI. Pharmaceutical Compositions of the Invention

The present invention also includes pharmaceutical compositions and formulations which include the iRNAs for use in the methods of the invention. In one embodiment, provided herein are pharmaceutical compositions containing an iRNA, as described herein, and a pharmaceutically acceptable carrier. The pharmaceutical compositions containing the iRNA are useful for treating primary hyperoxaluria. Such pharmaceutical compositions are formulated based on the mode of delivery.

The pharmaceutical compositions comprising RNAi agents of the invention may be, for example, solutions with or without a buffer, or compositions containing pharmaceutically acceptable carriers. Such compositions include, for example, aqueous or crystalline compositions, liposomal formulations, micellar formulations, emulsions, and gene therapy vectors.

In the methods of the invention, the RNAi agent may be administered in a solution. A free RNAi agent may be administered in an unbuffered solution, e.g., in saline or in water. Alternatively, the free siRNA may also be administered in a suitable buffer solution. The buffer solution may comprise acetate, citrate, prolamine, carbonate, or phosphate, or any combination thereof. In one embodiment, the buffer solution is phosphate buffered saline (PBS). The pH and osmolarity of the buffer solution containing the RNAi agent can be adjusted such that it is suitable for administering to a subject.

In some embodiments, the buffer solution further comprises an agent for controlling the osmolarity of the solution, such that the osmolarity is kept at a desired value, e.g., at the physiologic values of the human plasma. Solutes which can be added to the buffer solution to control the osmolarity include, but are not limited to, proteins, peptides, amino acids, non-metabolized polymers, vitamins, ions, sugars, metabolites, organic acids, lipids, or salts. In some embodiments, the agent for controlling the osmolarity of the solution is a salt. In certain embodiments, the agent for controlling the osmolarity of the solution is sodium chloride or potassium chloride.

In one embodiment, a pharmaceutical composition of the invention comprises a double stranded RNAi agent targeting HAO1 as described herein, e.g., lumasiran, e.g., about 94.5 mg of lumasiran, water for injection, e.g., 0.5 mL, and sodium hydroxide and/or phosphoric acid to adjust the pH to about 7.0. Such pharmaceutical compositions may be sterile and/or preservative free, for subcutaneous administration, and have an appearance that is clear, and/or colorless to yellow.

In some embodiments, the pharmaceutical compositions of the invention are pyrogen free or non-pyrogenic.

The pharmaceutical compositions of the invention may be administered in dosages sufficient to inhibit expression of a HAO1 gene.

The pharmaceutical compositions of the present invention can be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration can be topical (e.g., by a transdermal patch), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal, oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; subdermal, e.g., via an implanted device; or intracranial, e.g., by intraparenchymal, intrathecal or intraventricular, administration

The iRNA can be delivered in a manner to target a particular tissue, such as the liver.

Pharmaceutical compositions of the present invention include, but are not limited to, solutions, emulsions, and liposome-containing formulations. These compositions can be generated from a variety of components that include, but are not limited to, preformed liquids, self-emulsifying solids and self-emulsifying semisolids.

The pharmaceutical formulations of the present invention, which can conveniently be presented in unit dosage form, can be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general, the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.

The compositions of the present invention can be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present invention can also be formulated as suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions can further contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension can also contain stabilizers.

The compositions of the present invention can be formulated for oral administration; parenteral, intraparenchymal (into the brain), intrathecal, intraventricular or intrahepatic administration, and/or topical administration.

Compositions and formulations for oral administration include powders or granules, microparticulates, nanoparticulates, suspensions or solutions in water or non-aqueous media, capsules, gel capsules, sachets, tablets or minitablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders can be desirable. In some embodiments, oral formulations are those in which dsRNAs featured in the invention are administered in conjunction with one or more penetration enhancer surfactants and chelators. Suitable surfactants include fatty acids and/or esters or salts thereof, bile acids and/or salts thereof. Suitable bile acids/salts include chenodeoxycholic acid (CDCA) and ursodeoxychenodeoxycholic acid (UDCA), cholic acid, dehydrocholic acid, deoxycholic acid, glucholic acid, glycholic acid, glycodeoxycholic acid, taurocholic acid, taurodeoxycholic acid, sodium tauro-24,25-dihydro-fusidate and sodium glycodihydrofusidate. Suitable fatty acids include arachidonic acid, undecanoic acid, oleic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a monoglyceride, a diglyceride or a pharmaceutically acceptable salt thereof (e.g., sodium). In some embodiments, combinations of penetration enhancers are used, for example, fatty acids/salts in combination with bile acids/salts. One exemplary combination is the sodium salt of lauric acid, capric acid and UDCA. Further penetration enhancers include polyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether. DsRNAs featured in the invention can be delivered orally, in granular form including sprayed dried particles, or complexed to form micro or nanoparticles. DsRNA complexing agents include poly-amino acids; polyimines; polyacrylates; polyalkylacrylates, polyoxethanes, polyalkylcyanoacrylates; cationized gelatins, albumins, starches, acrylates, polyethyleneglycols (PEG) and starches; polyalkylcyanoacrylates; DEAE-derivatized polyimines, pollulans, celluloses and starches. Suitable complexing agents include chitosan, N-trimethylchitosan, poly-L-lysine, polyhistidine, polyornithine, polyspermines, protamine, polyvinylpyridine, polythiodiethylaminomethylethylene P(TDAE), polyaminostyrene (e.g., p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate), poly(butylcyanoacrylate), poly(isobutylcyanoacrylate), poly(isohexylcynaoacrylate), DEAE-methacrylate, DEAE-hexylacrylate, DEAE-acrylamide, DEAE-albumin and DEAE-dextran, polymethylacrylate, polyhexylacrylate, poly(D,L-lactic acid), poly(DL-lactic-co-glycolic acid (PLGA), alginate, and polyethyleneglycol (PEG). Oral formulations for dsRNAs and their preparation are described in detail in U.S. Pat. No. 6,887,906, US Publn. No. 20030027780, and U.S. Pat. No. 6,747,014, each of which is incorporated herein by reference.

Compositions and formulations for parenteral, intraparenchymal (into the brain), intrathecal, intraventricular or intrahepatic administration can include sterile aqueous solutions which can also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.

Pharmaceutical compositions and formulations for topical administration can include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like can be necessary or desirable. Coated condoms, gloves and the like can also be useful. Suitable topical formulations include those in which the iRNAs featured in the invention are in admixture with a topical delivery agent such as lipids, liposomes, fatty acids, fatty acid esters, steroids, chelating agents and surfactants. Suitable lipids and liposomes include neutral (e.g., dioleoylphosphatidyl DOPE ethanolamine, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline) negative (e.g., dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g., dioleoyltetramethylaminopropyl DOTAP and dioleoylphosphatidyl ethanolamine DOTMA). iRNAs featured in the invention can be encapsulated within liposomes or can form complexes thereto, in particular to cationic liposomes. Alternatively, iRNAs can be complexed to lipids, in particular to cationic lipids. Suitable fatty acids and esters include but are not limited to arachidonic acid, oleic acid, eicosanoic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a C₁₋₂₀ alkyl ester (e.g., isopropylmyristate IPM), monoglyceride, diglyceride or pharmaceutically acceptable salt thereof). Topical formulations are described in detail in U.S. Pat. No. 6,747,014, which is incorporated herein by reference.

A. iRNA Formulations Comprising Membranous Molecular Assemblies

An iRNA for use in the compositions and methods of the invention can be formulated for delivery in a membranous molecular assembly, e.g., a liposome or a micelle. As used herein, the term “liposome” refers to a vesicle composed of amphiphilic lipids arranged in at least one bilayer, e.g., one bilayer or a plurality of bilayers. Liposomes include unilamellar and multilamellar vesicles that have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the iRNA composition. The lipophilic material isolates the aqueous interior from an aqueous exterior, which typically does not include the iRNA composition, although in some examples, it may. Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomal bilayer fuses with bilayer of the cellular membranes. As the merging of the liposome and cell progresses, the internal aqueous contents that include the iRNA are delivered into the cell where the iRNA can specifically bind to a target RNA and can mediate RNAi. In some cases the liposomes are also specifically targeted, e.g., to direct the iRNA to particular cell types.

A liposome containing a RNAi agent can be prepared by a variety of methods. In one example, the lipid component of a liposome is dissolved in a detergent so that micelles are formed with the lipid component. For example, the lipid component can be an amphipathic cationic lipid or lipid conjugate. The detergent can have a high critical micelle concentration and may be nonionic. Exemplary detergents include cholate, CHAPS, octylglucoside, deoxycholate, and lauroyl sarcosine. The RNAi agent preparation is then added to the micelles that include the lipid component. The cationic groups on the lipid interact with the RNAi agent and condense around the RNAi agent to form a liposome. After condensation, the detergent is removed, e.g., by dialysis, to yield a liposomal preparation of RNAi agent.

If necessary a carrier compound that assists in condensation can be added during the condensation reaction, e.g., by controlled addition. For example, the carrier compound can be a polymer other than a nucleic acid (e.g., spermine or spermidine). pH can also adjusted to favor condensation.

Methods for producing stable polynucleotide delivery vehicles, which incorporate a polynucleotide/cationic lipid complex as structural components of the delivery vehicle, are further described in, e.g., WO 96/37194, the entire contents of which are incorporated herein by reference. Liposome formation can also include one or more aspects of exemplary methods described in Felgner, P. L. et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987; U.S. Pat. Nos. 4,897,355; 5,171,678; Bangham, et al. M. Mol. Biol. 23:238, 1965; Olson, et al. Biochim. Biophys. Acta 557:9, 1979; Szoka, et al. Proc. Natl. Acad. Sci. 75: 4194, 1978; Mayhew, et al. Biochim. Biophys. Acta 775:169, 1984; Kim, et al. Biochim. Biophys. Acta 728:339, 1983; and Fukunaga, et al. Endocrinol. 115:757, 1984. Commonly used techniques for preparing lipid aggregates of appropriate size for use as delivery vehicles include sonication and freeze-thaw plus extrusion (see, e.g., Mayer, et al. Biochim. Biophys. Acta 858:161, 1986). Microfluidization can be used when consistently small (50 to 200 nm) and relatively uniform aggregates are desired (Mayhew, et al. Biochim. Biophys. Acta 775:169, 1984). These methods are readily adapted to packaging RNAi agent preparations into liposomes.

Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes which interact with the negatively charged nucleic acid molecules to form a stable complex. The positively charged nucleic acid/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al., Biochem. Biophys. Res. Commun., 1987, 147, 980-985).

Liposomes which are pH-sensitive or negatively-charged, entrap nucleic acids rather than complex with it. Since both the nucleic acid and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some nucleic acid is entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes have been used to deliver nucleic acids encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 1992, 19, 269-274).

One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine. Neutral liposome compositions, for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC). Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC. Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.

Examples of other methods to introduce liposomes into cells in vitro and in vivo include U.S. Pat. Nos. 5,283,185; 5,171,678; WO 94/00569; WO 93/24640; WO 91/16024; Felgner, J. Biol. Chem. 269:2550, 1994; Nabel, Proc. Natl. Acad. Sci. 90:11307, 1993; Nabel, Human Gene Ther. 3:649, 1992; Gershon, Biochem. 32:7143, 1993; and Strauss EMBO J. 11:417, 1992.

Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome™ I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome™ II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the dermis of mouse skin. Results indicated that such non-ionic liposomal systems were effective in facilitating the deposition of cyclosporine A into different layers of the skin (Hu et al. S.T.P. Pharma. Sci., 1994, 4(6) 466).

Liposomes also include “sterically stabilized” liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids that, when incorporated into liposomes, result in enhanced circulation lifetimes relative to liposomes lacking such specialized lipids. Examples of sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside G_(M1), or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety. While not wishing to be bound by any particular theory, it is thought in the art that, at least for sterically stabilized liposomes containing gangliosides, sphingomyelin, or PEG-derivatized lipids, the enhanced circulation half-life of these sterically stabilized liposomes derives from a reduced uptake into cells of the reticuloendothelial system (RES) (Allen et al., FEBS Letters, 1987, 223, 42; Wu et al., Cancer Research, 1993, 53, 3765).

Various liposomes comprising one or more glycolipids are known in the art. Papahadjopoulos et al. (Ann. N.Y. Acad. Sci., 1987, 507, 64) reported the ability of monosialoganglioside G_(M1), galactocerebroside sulfate and phosphatidylinositol to improve blood half-lives of liposomes. These findings were expounded upon by Gabizon et al. (Proc. Natl. Acad. Sci. U.S.A., 1988, 85, 6949). U.S. Pat. No. 4,837,028 and WO 88/04924, both to Allen et al., disclose liposomes comprising (1) sphingomyelin and (2) the ganglioside G_(M1) or a galactocerebroside sulfate ester. U.S. Pat. No. 5,543,152 (Webb et al.) discloses liposomes comprising sphingomyelin. Liposomes comprising 1,2-sn-dimyristoylphosphatidylcholine are disclosed in WO 97/13499 (Lim et al).

In one embodiment, cationic liposomes are used. Cationic liposomes possess the advantage of being able to fuse to the cell membrane. Non-cationic liposomes, although not able to fuse as efficiently with the plasma membrane, are taken up by macrophages in vivo and can be used to deliver RNAi agents to macrophages.

Further advantages of liposomes include: liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated RNAi agents in their internal compartments from metabolism and degradation (Rosoff, in “Pharmaceutical Dosage Forms,” Lieberman, Rieger and Banker (Eds.), 1988, volume 1, p. 245). Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.

A positively charged synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA) can be used to form small liposomes that interact spontaneously with nucleic acid to form lipid-nucleic acid complexes which are capable of fusing with the negatively charged lipids of the cell membranes of tissue culture cells, resulting in delivery of RNAi agent (see, e.g., Felgner, P. L. et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987 and U.S. Pat. No. 4,897,355 for a description of DOTMA and its use with DNA).

A DOTMA analogue, 1,2-bis(oleoyloxy)-3-(trimethylammonia)propane (DOTAP) can be used in combination with a phospholipid to form DNA-complexing vesicles. Lipofectin™ Bethesda Research Laboratories, Gaithersburg, Md.) is an effective agent for the delivery of highly anionic nucleic acids into living tissue culture cells that comprise positively charged DOTMA liposomes which interact spontaneously with negatively charged polynucleotides to form complexes. When enough positively charged liposomes are used, the net charge on the resulting complexes is also positive. Positively charged complexes prepared in this way spontaneously attach to negatively charged cell surfaces, fuse with the plasma membrane, and efficiently deliver functional nucleic acids into, for example, tissue culture cells. Another commercially available cationic lipid, 1,2-bis(oleoyloxy)-3,3-(trimethylammonia)propane (“DOTAP”) (Boehringer Mannheim, Indianapolis, Indiana) differs from DOTMA in that the oleoyl moieties are linked by ester, rather than ether linkages.

Other reported cationic lipid compounds include those that have been conjugated to a variety of moieties including, for example, carboxyspermine which has been conjugated to one of two types of lipids and includes compounds such as 5-carboxyspermylglycine dioctaoleoylamide (“DOGS”) (Transfectam™, Promega, Madison, Wisconsin) and dipalmitoylphosphatidylethanolamine 5-carboxyspermyl-amide (“DPPES”) (see, e.g., U.S. Pat. No. 5,171,678).

Another cationic lipid conjugate includes derivatization of the lipid with cholesterol (“DC-Chol”) which has been formulated into liposomes in combination with DOPE (See, Gao, X. and Huang, L., Biochim. Biophys. Res. Commun. 179:280, 1991). Lipopolylysine, made by conjugating polylysine to DOPE, has been reported to be effective for transfection in the presence of serum (Zhou, X. et al., Biochim. Biophys. Acta 1065:8, 1991). For certain cell lines, these liposomes containing conjugated cationic lipids, are said to exhibit lower toxicity and provide more efficient transfection than the DOTMA-containing compositions. Other commercially available cationic lipid products include DMRIE and DMRIE-HP (Vical, La Jolla, California) and Lipofectamine (DOSPA) (Life Technology, Inc., Gaithersburg, Maryland). Other cationic lipids suitable for the delivery of oligonucleotides are described in WO 98/39359 and WO 96/37194.

Liposomal formulations are particularly suited for topical administration, liposomes present several advantages over other formulations. Such advantages include reduced side effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer RNAi agent into the skin. In some implementations, liposomes are used for delivering RNAi agent to epidermal cells and also to enhance the penetration of RNAi agent into dermal tissues, e.g., into skin. For example, the liposomes can be applied topically. Topical delivery of drugs formulated as liposomes to the skin has been documented (see, e.g., Weiner et al., Journal of Drug Targeting, 1992, vol. 2, 405-410 and du Plessis et al., Antiviral Research, 18, 1992, 259-265; Mannino, R. J. and Fould-Fogerite, S., Biotechniques 6:682-690, 1988; Itani, T. et al. Gene 56:267-276. 1987; Nicolau, C. et al. Meth. Enz. 149:157-176, 1987; Straubinger, R. M. and Papahadjopoulos, D. Meth. Enz. 101:512-527, 1983; Wang, C. Y. and Huang, L., Proc. Natl. Acad. Sci. USA 84:7851-7855, 1987).

Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver a drug into the dermis of mouse skin. Such formulations with RNAi agent are useful for treating a dermatological disorder.

Liposomes that include iRNA can be made highly deformable. Such deformability can enable the liposomes to penetrate through pore that are smaller than the average radius of the liposome. For example, transferosomes are a type of deformable liposomes. Transferosomes can be made by adding surface edge activators, usually surfactants, to a standard liposomal composition. Transferosomes that include RNAi agent can be delivered, for example, subcutaneously by infection in order to deliver RNAi agent to keratinocytes in the skin. In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. In addition, due to the lipid properties, these transferosomes can be self-optimizing (adaptive to the shape of pores, e.g., in the skin), self-repairing, and can frequently reach their targets without fragmenting, and often self-loading.

Other formulations amenable to the present invention are described in U.S. provisional application Ser. No. 61/018,616, filed Jan. 2, 2008; 61/018,611, filed Jan. 2, 2008; 61/039,748, filed Mar. 26, 2008; 61/047,087, filed Apr. 22, 2008 and 61/051,528, filed May 8, 2008. PCT application no PCT/US2007/080331, filed Oct. 3, 2007 also describes formulations that are amenable to the present invention.

Transferosomes are yet another type of liposomes, and are highly deformable lipid aggregates which are attractive candidates for drug delivery vehicles. Transferosomes can be described as lipid droplets which are so highly deformable that they are easily able to penetrate through pores which are smaller than the droplet. Transferosomes are adaptable to the environment in which they are used, e.g., they are self-optimizing (adaptive to the shape of pores in the skin), self-repairing, frequently reach their targets without fragmenting, and often self-loading. To make transferosomes it is possible to add surface edge-activators, usually surfactants, to a standard liposomal composition. Transferosomes have been used to deliver serum albumin to the skin. The transferosome-mediated delivery of serum albumin has been shown to be as effective as subcutaneous injection of a solution containing serum albumin.

Surfactants find wide application in formulations such as emulsions (including microemulsions) and liposomes. The most common way of classifying and ranking the properties of the many different types of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile balance (HLB). The nature of the hydrophilic group (also known as the “head”) provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

If the surfactant molecule is not ionized, it is classified as a nonionic surfactant. Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure. Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class. The polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.

If the surfactant molecule carries a negative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic. Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates. The most important members of the anionic surfactant class are the alkyl sulfates and the soaps.

If the surfactant molecule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic. Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.

If the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.

The use of surfactants in drug products, formulations and in emulsions has been reviewed (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

The iRNA for use in the methods of the invention can also be provided as micellar formulations. “Micelles” are defined herein as a particular type of molecular assembly in which amphipathic molecules are arranged in a spherical structure such that all the hydrophobic portions of the molecules are directed inward, leaving the hydrophilic portions in contact with the surrounding aqueous phase. The converse arrangement exists if the environment is hydrophobic.

A mixed micellar formulation suitable for delivery through transdermal membranes may be prepared by mixing an aqueous solution of the siRNA composition, an alkali metal C₈ to C₂₂ alkyl sulphate, and a micelle forming compounds. Exemplary micelle forming compounds include lecithin, hyaluronic acid, pharmaceutically acceptable salts of hyaluronic acid, glycolic acid, lactic acid, chamomile extract, cucumber extract, oleic acid, linoleic acid, linolenic acid, monoolein, monooleates, monolaurates, borage oil, evening of primrose oil, menthol, trihydroxy oxo cholanyl glycine and pharmaceutically acceptable salts thereof, glycerin, polyglycerin, lysine, polylysine, triolein, polyoxyethylene ethers and analogues thereof, polidocanol alkyl ethers and analogues thereof, chenodeoxycholate, deoxycholate, and mixtures thereof. The micelle forming compounds may be added at the same time or after addition of the alkali metal alkyl sulphate. Mixed micelles will form with substantially any kind of mixing of the ingredients but vigorous mixing in order to provide smaller size micelles.

In one method a first micellar composition is prepared which contains the siRNA composition and at least the alkali metal alkyl sulphate. The first micellar composition is then mixed with at least three micelle forming compounds to form a mixed micellar composition. In another method, the micellar composition is prepared by mixing the siRNA composition, the alkali metal alkyl sulphate and at least one of the micelle forming compounds, followed by addition of the remaining micelle forming compounds, with vigorous mixing.

Phenol and/or m-cresol may be added to the mixed micellar composition to stabilize the formulation and protect against bacterial growth. Alternatively, phenol and/or m-cresol may be added with the micelle forming ingredients. An isotonic agent such as glycerin may also be added after formation of the mixed micellar composition.

For delivery of the micellar formulation as a spray, the formulation can be put into an aerosol dispenser and the dispenser is charged with a propellant. The propellant, which is under pressure, is in liquid form in the dispenser. The ratios of the ingredients are adjusted so that the aqueous and propellant phases become one, i.e., there is one phase. If there are two phases, it is necessary to shake the dispenser prior to dispensing a portion of the contents, e.g., through a metered valve. The dispensed dose of pharmaceutical agent is propelled from the metered valve in a fine spray.

Propellants may include hydrogen-containing chlorofluorocarbons, hydrogen-containing fluorocarbons, dimethyl ether and diethyl ether. In certain embodiments, HFA 134a (1,1,1,2 tetrafluoroethane) may be used.

The specific concentrations of the essential ingredients can be determined by relatively straightforward experimentation. For absorption through the oral cavities, it is often desirable to increase, e.g., at least double or triple, the dosage for through injection or administration through the gastrointestinal tract.

B. Lipid Particles

The iRNAs, e.g., dsRNAs of in the invention may be fully encapsulated in a lipid formulation, e.g., a LNP, or other nucleic acid-lipid particle.

As used herein, the term “LNP” refers to a stable nucleic acid-lipid particle. LNPs contain a cationic lipid, a non-cationic lipid, and a lipid that prevents aggregation of the particle (e.g., a PEG-lipid conjugate). LNPs are extremely useful for systemic applications, as they exhibit extended circulation lifetimes following intravenous (i.v.) injection and accumulate at distal sites (e.g., sites physically separated from the administration site). LNPs include “pSPLP,” which include an encapsulated condensing agent-nucleic acid complex as set forth in PCT Publication No. WO 00/03683. The particles of the present invention typically have a mean diameter of about 50 nm to about 150 nm, more typically about 60 nm to about 130 nm, more typically about 70 nm to about 110 nm, most typically about 70 nm to about 90 nm, and are substantially nontoxic. In addition, the nucleic acids when present in the nucleic acid-lipid particles of the present invention are resistant in aqueous solution to degradation with a nuclease. Nucleic acid-lipid particles and their method of preparation are disclosed in, e.g., U.S. Pat. Nos. 5,976,567; 5,981,501; 6,534,484; 6,586,410; 6,815,432; U.S. Publication No. 2010/0324120 and PCT Publication No. WO 96/40964.

In one embodiment, the lipid to drug ratio (mass/mass ratio) (e.g., lipid to dsRNA ratio) will be in the range of from about 1:1 to about 50:1, from about 1:1 to about 25:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, or about 6:1 to about 9:1. Ranges intermediate to the above recited ranges are also contemplated to be part of the invention.

The cationic lipid can be, for example, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N-(I-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), N-(I-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-dimethyl-2,3-dioleyloxy)propylamine (DODMA), 1,2-DiLinoleyloxy-N,N-dimethylaminopropane (DLinDMA), 1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA), 1,2-Dilinoleylcarbamoyloxy-3-dimethylaminopropane (DLin-C-DAP), 1,2-Dilinoleyoxy-3-(dimethylamino)acetoxypropane (DLin-DAC), 1,2-Dilinoleyoxy-3-morpholinopropane (DLin-MA), 1,2-Dilinoleoyl-3-dimethylaminopropane (DLinDAP), 1,2-Dilinoleylthio-3-dimethylaminopropane (DLin-S-DMA), 1-Linoleoyl-2-linoleyloxy-3-dimethylaminopropane (DLin-2-DMAP), 1,2-Dilinoleyloxy-3-trimethylaminopropane chloride salt (DLin-TMA.Cl), 1,2-Dilinoleoyl-3-trimethylaminopropane chloride salt (DLin-TAP.Cl), 1,2-Dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPZ), or 3-(N,N-Dilinoleylamino)-1,2-propanediol (DLinAP), 3-(N,N-Dioleylamino)-1,2-propanedio (DOAP), 1,2-Dilinoleyloxo-3-(2-N,N-dimethylamino)ethoxypropane (DLin-EG-DMA), 1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLinDMA), 2,2-Dilinoleyl-4-dimethylaminomethyl-[1,3]-dioxolane (DLin-K-DMA) or analogs thereof, (3aR,5s,6aS)-N,N-dimethyl-2,2-di((9Z,12Z)-octadeca-9,12-dienyl)tetrahydro-3aH-cyclopenta[d][1,3]dioxol-5-amine (ALN100), (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate (MC3), 1,1′-(2-(4-(2-((2-(bis(2-hydroxydodecyl)amino)ethyl)(2-hydroxydodecyl)amino)ethyl)piperazin-1-yl)ethylazanediyl)didodecan-2-ol (Tech GI), or a mixture thereof. The cationic lipid can comprise from about 20 mol % to about 50 mol % or about 40 mol % of the total lipid present in the particle.

In another embodiment, the compound 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane can be used to prepare lipid-siRNA nanoparticles. Synthesis of 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane is described in International application no. PCT/US2009/061897, published as WO/2010/048536, which is herein incorporated by reference.

In one embodiment, the lipid-siRNA particle includes 40% 2, 2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane: 10% DSPC: 40% Cholesterol: 10% PEG-C-DOMG (mole percent) with a particle size of 63.0±20 nm and a 0.027 siRNA/Lipid Ratio.

The ionizable/non-cationic lipid can be an anionic lipid or a neutral lipid including, but not limited to, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl-phosphatidylethanolamine 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (DOPE-mal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DMPE), distearoyl-phosphatidyl-ethanolamine (DSPE), 16-O-monomethyl PE, 16-O-dimethyl PE, 18-1-trans PE, 1-stearoyl-2-oleoyl-phosphatidyethanolamine (SOPE), cholesterol, or a mixture thereof. The non-cationic lipid can be from about 5 mol % to about 90 mol %, about 10 mol %, or about 58 mol % if cholesterol is included, of the total lipid present in the particle.

The conjugated lipid that inhibits aggregation of particles can be, for example, a polyethyleneglycol (PEG)-lipid including, without limitation, a PEG-diacylglycerol (DAG), a PEG-dialkyloxypropyl (DAA), a PEG-phospholipid, a PEG-ceramide (Cer), or a mixture thereof. The PEG-DAA conjugate can be, for example, a PEG-dilauryloxypropyl (Ci₂), a PEG-dimyristyloxypropyl (Ci₄), a PEG-dipalmityloxypropyl (Ci₆), or a PEG-distearyloxypropyl (C]₈). The conjugated lipid that prevents aggregation of particles can be from 0 mol % to about 20 mol % or about 2 mol % of the total lipid present in the particle.

In some embodiments, the nucleic acid-lipid particle further includes cholesterol at, e.g., about 10 mol % to about 60 mol % or about 48 mol % of the total lipid present in the particle.

In one embodiment, the lipidoid ND98·4HCl (MW 1487) (see U.S. patent application Ser. No. 12/056,230, filed Mar. 26, 2008, which is incorporated herein by reference), Cholesterol (Sigma-Aldrich), and PEG-Ceramide C16 (Avanti Polar Lipids) can be used to prepare lipid-dsRNA nanoparticles (i.e., LNP01 particles). Stock solutions of each in ethanol can be prepared as follows: ND98, 133 mg/ml; Cholesterol, 25 mg/ml, PEG-Ceramide C16, 100 mg/ml. The ND98, Cholesterol, and PEG-Ceramide C16 stock solutions can then be combined in a, e.g., 42:48:10 molar ratio. The combined lipid solution can be mixed with aqueous dsRNA (e.g., in sodium acetate pH 5) such that the final ethanol concentration is about 35-45% and the final sodium acetate concentration is about 100-300 mM. Lipid-dsRNA nanoparticles typically form spontaneously upon mixing. Depending on the desired particle size distribution, the resultant nanoparticle mixture can be extruded through a polycarbonate membrane (e.g., 100 nm cut-oft) using, for example, a thermobarrel extruder, such as Lipex Extruder (Northern Lipids, Mc). In some cases, the extrusion step can be omitted. Ethanol removal and simultaneous buffer exchange can be accomplished by, for example, dialysis or tangential flow filtration. Buffer can be exchanged with, for example, phosphate buffered saline (PBS) at about pH 7, e.g., about pH 6.9, about pH 7.0, about pH 7. 1, about pH 7.2, about pH 7.3, or about pH 7.4. LNP01 formulations are described, e.g., in International Application Publication No. WO 2008/042973, which is hereby incorporated by reference.

Additional exemplary lipid-dsRNA formulations are described in Table A.

TABLE A Exemplary lipid dsRNA formulations cationic lipid/non-cationic lipid/cholesterol/PEG-lipid conjugate Ionizable/Cationic Lipid Lipid:siRNA ratio LNP_DLinDMA 1,2-Dilinolenyloxy-N,N- DLinDMA/DPPC/Cholesterol/PEG-cDMA dimethylaminopropane (DLinDMA) (57.1/7.1/34.4/1.4) lipid:siRNA~7:1 2-XTC 2,2-Dilinoleyl-4-dimethylaminoethyl- XTC/DPPC/Cholesterol/PEG-cDMA [1,3]-dioxolane (XTC) 57.1/7.1/34.4/1.4 lipid:siRNA~7:1 LNP05 2,2-Dilinoleyl-4-dimethylaminoethyl- XTC/DSPC/Cholesterol/PEG-DMG [1,3]-dioxolane (XTC) 57.5/7.5/31.5/3.5 lipid:siRNA~6:1 LNP06 2,2-Dilinoleyl-4-dimethylaminoethyl- XTC/DSPC/Cholesterol/PEG-DMG [1,3]-dioxolane (XTC) 57.5/7.5/31.5/3.5 lipid:siRNA~11:1 LNP07 2,2-Dilinoleyl-4-dimethylaminoethyl- XTC/DSPC/Cholesterol/PEG-DMG [1,3]-dioxolane (XTC) 60/7.5/31/1.5, lipid:siRNA~6:1 LNP08 2,2-Dilinoleyl-4-dimethylaminoethyl- XTC/DSPC/Cholesterol/PEG-DMG [1,3]-dioxolane (XTC) 60/7.5/31/1.5, lipid:siRNA~11:1 LNP09 2,2-Dilinoleyl-4-dimethylaminoethyl- XTC/DSPC/Cholesterol/PEG-DMG [1,3]-dioxolane (XTC) 50/10/38.5/1.5 Lipid:siRNA 10:1 LNP10 (3aR,5s,6aS)-N,N-dimethyl-2,2- ALN100/DSPC/Cholesterol/PEG-DMG di((9Z,12Z)-octadeca-9,12- 50/10/38.5/1.5 dienyl)tetrahydro-3aH- Lipid:siRNA 10:1 cyclopenta[d][1,3]dioxol-5-amine (ALN100) LNP11 (6Z,9Z,28Z,31Z)-heptatriaconta- MC-3/DSPC/Cholesterol/PEG-DMG 6,9,28,31-tetraen-19-yl 4- 50/10/38.5/1.5 (dimethylamino)butanoate (MC3) Lipid:siRNA 10:1 LNP12 1,1′-(2-(4-(2-((2-(bis(2- Tech G1/DSPC/Cholesterol/PEG-DMG hydroxydodecyl)amino)ethyl)(2- 50/10/38.5/1.5 hydroxydodecyl)amino)ethyl)piperazin- Lipid:siRNA 10:1 1-yl)ethylazanediyl)didodecan-2-ol (C12-200> LNP13 XTC XTC/DSPC/Chol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA: 33:1 LNP14 MC3 MC3/DSPC/Chol/PEG-DMG 40/15/40/5 Lipid:siRNA: 11:1 LNP15 MC3 MC3/DSPC/Chol/PEG-DSG/GalNAc- PEG-DSG 50/10/35/4.5/0.5 Lipid:siRNA: 11:1 LNP16 MC3 MC3/DSPC/Chol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA: 7:1 LNP17 MC3 MC3/DSPC/Chol/PEG-DSG 50/10/38.5/1.5 Lipid:siRNA: 10:1 LNP18 MC3 MC3/DSPC/Chol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA: 12:1 LNP19 MC3 MC3/DSPC/Chol/PEG-DMG 50/10/35/5 Lipid:siRNA: 8:1 LNP20 MC3 MC3/DSPC/Chol/PEG-DPG 50/10/38.5/1.5 Lipid:siRNA: 10:1 LNP21 C12-200 C12-200/DSPC/Chol/PEG-DSG 50/10/38.5/1.5 Lipid:siRNA: 7:1 LNP22 XTC XTC/DSPC/Chol/PEG-DSG 50/10/38.5/1.5 Lipid:siRNA: 10:1

Abbreviations in Table A include the following: DSPC: distearoylphosphatidylcholine; DPPC: dipalmitoylphosphatidylcholine; PEG-DMG: PEG-didimyristoyl glycerol (C14-PEG, or PEG-C14) (PEG with avg mol wt of 2000); PEG-DSG: PEG-distyryl glycerol (C18-PEG, or PEG-C18) (PEG with avg mol wt of 2000); PEG-cDMA: PEG-carbamoyl-1,2-dimyristyloxypropylamine (PEG with avg mol wt of 2000).

DLinDMA (1,2-Dilinolenyloxy-N,N-dimethylaminopropane) comprising formulations are described in International Publication No. WO2009/127060, filed Apr. 15, 2009, which is hereby incorporated by reference.

XTC comprising formulations are described, e.g., in U.S. Provisional Ser. No. 61/148,366, filed Jan. 29, 2009; U.S. Provisional Ser. No. 61/156,851, filed Mar. 2, 2009; U.S. Provisional Serial No. filed Jun. 10, 2009; U.S. Provisional Ser. No. 61/228,373, filed Jul. 24, 2009; U.S. Provisional Ser. No. 61/239,686, filed Sep. 3, 2009, and International Application No. PCT/US2010/022614, filed Jan. 29, 2010, which are hereby incorporated by reference.

MC3 comprising formulations are described, e.g., in U.S. Publication No. 2010/0324120, filed Jun. 10, 2010, the entire contents of which are hereby incorporated by reference.

ALNY-100 comprising formulations are described, e.g., International patent application number PCT/US09/63933, filed on Nov. 10, 2009, which is hereby incorporated by reference.

C12-200 comprising formulations are described in U.S. Provisional Ser. No. 61/175,770, filed May 5, 2009 and International Application No. PCT/US10/33777, filed May 5, 2010, which are hereby incorporated by reference.

C. Additional Formulations

i. Emulsions

The compositions of the present invention can be prepared and formulated as emulsions.

Emulsions are typically heterogeneous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 μm in diameter (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, NY; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., Volume 1, p. 245; Block in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 2, p. 335; Higuchi et al., in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 301). Emulsions are often biphasic systems comprising two immiscible liquid phases intimately mixed and dispersed with each other. In general, emulsions can be of either the water-in-oil (w/o) or the oil-in-water (o/w) variety. When an aqueous phase is finely divided into and dispersed as minute droplets into a bulk oily phase, the resulting composition is called a water-in-oil (w/o) emulsion. Alternatively, when an oily phase is finely divided into and dispersed as minute droplets into a bulk aqueous phase, the resulting composition is called an oil-in-water (o/w) emulsion. Emulsions can contain additional components in addition to the dispersed phases, and the active drug which can be present as a solution in either the aqueous phase, oily phase or itself as a separate phase. Pharmaceutical excipients such as emulsifiers, stabilizers, dyes, and anti-oxidants can also be present in emulsions as needed. Pharmaceutical emulsions can also be multiple emulsions that are comprised of more than two phases such as, for example, in the case of oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions. Such complex formulations often provide certain advantages that simple binary emulsions do not. Multiple emulsions in which individual oil droplets of an o/w emulsion enclose small water droplets constitute a w/o/w emulsion. Likewise a system of oil droplets enclosed in globules of water stabilized in an oily continuous phase provides an o/w/o emulsion.

Emulsions are characterized by little or no thermodynamic stability. Often, the dispersed or discontinuous phase of the emulsion is well dispersed into the external or continuous phase and maintained in this form through the means of emulsifiers or the viscosity of the formulation. Either of the phases of the emulsion can be a semisolid or a solid, as is the case of emulsion-style ointment bases and creams. Other means of stabilizing emulsions entail the use of emulsifiers that can be incorporated into either phase of the emulsion. Emulsifiers can broadly be classified into four categories: synthetic surfactants, naturally occurring emulsifiers, absorption bases, and finely dispersed solids (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, NY; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

Synthetic surfactants, also known as surface active agents, have found wide applicability in the formulation of emulsions and have been reviewed in the literature (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, NY; Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199). Surfactants are typically amphiphilic and comprise a hydrophilic and a hydrophobic portion. The ratio of the hydrophilic to the hydrophobic nature of the surfactant has been termed the hydrophile/lipophile balance (HLB) and is a valuable tool in categorizing and selecting surfactants in the preparation of formulations. Surfactants can be classified into different classes based on the nature of the hydrophilic group: nonionic, anionic, cationic and amphoteric (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, NY Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285).

Naturally occurring emulsifiers used in emulsion formulations include lanolin, beeswax, phosphatides, lecithin and acacia. Absorption bases possess hydrophilic properties such that they can soak up water to form w/o emulsions yet retain their semisolid consistencies, such as anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations. These include polar inorganic solids, such as heavy metal hydroxides, nonswelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and nonpolar solids such as carbon or glyceryl tristearate.

A large variety of non-emulsifying materials are also included in emulsion formulations and contribute to the properties of emulsions. These include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives and antioxidants (Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

Hydrophilic colloids or hydrocolloids include naturally occurring gums and synthetic polymers such as polysaccharides (for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth), cellulose derivatives (for example, carboxymethylcellulose and carboxypropylcellulose), and synthetic polymers (for example, carbomers, cellulose ethers, and carboxyvinyl polymers). These disperse or swell in water to form colloidal solutions that stabilize emulsions by forming strong interfacial films around the dispersed-phase droplets and by increasing the viscosity of the external phase.

Since emulsions often contain a number of ingredients such as carbohydrates, proteins, sterols and phosphatides that can readily support the growth of microbes, these formulations often incorporate preservatives. Commonly used preservatives included in emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid. Antioxidants are also commonly added to emulsion formulations to prevent deterioration of the formulation. Antioxidants used can be free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.

The application of emulsion formulations via dermatological, oral and parenteral routes and methods for their manufacture have been reviewed in the literature (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, NY; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Emulsion formulations for oral delivery have been very widely used because of ease of formulation, as well as efficacy from an absorption and bioavailability standpoint (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, NY; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Mineral-oil base laxatives, oil-soluble vitamins and high fat nutritive preparations are among the materials that have commonly been administered orally as o/w emulsions.

ii. Microemulsions

In one embodiment of the present invention, the compositions of iRNAs and nucleic acids are formulated as microemulsions. A microemulsion can be defined as a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, NY; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Typically microemulsions are systems that are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a fourth component, generally an intermediate chain-length alcohol to form a transparent system. Therefore, microemulsions have also been described as thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules (Leung and Shah, in: Controlled Release of Drugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH Publishers, New York, pages 185-215). Microemulsions commonly are prepared via a combination of three to five components that include oil, water, surfactant, cosurfactant and electrolyte. Whether the microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the properties of the oil and surfactant used and on the structure and geometric packing of the polar heads and hydrocarbon tails of the surfactant molecules (Schott, in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 271).

The phenomenological approach utilizing phase diagrams has been extensively studied and has yielded a comprehensive knowledge, to one skilled in the art, of how to formulate microemulsions (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8th ed.), New York, NY; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335). Compared to conventional emulsions, microemulsions offer the advantage of solubilizing water-insoluble drugs in a formulation of thermodynamically stable droplets that are formed spontaneously.

Surfactants used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750), decaglycerol decaoleate (DAO750), alone or in combination with cosurfactants. The cosurfactant, usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules. Microemulsions can, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art. The aqueous phase can typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol. The oil phase can include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.

Microemulsions are particularly of interest from the standpoint of drug solubilization and the enhanced absorption of drugs. Lipid based microemulsions (both o/w and w/o) have been proposed to enhance the oral bioavailability of drugs, including peptides (see e.g., U.S. Pat. Nos. 6,191,105; 7,063,860; 7,070,802; 7,157,099; Constantinides et al., Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find. Exp. Clin. Pharmacol., 1993, 13, 205). Microemulsions afford advantages of improved drug solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (see e.g., U.S. Pat. Nos. 6,191,105; 7,063,860; 7,070,802; 7,157,099; Constantinides et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm. Sci., 1996, 85, 138-143). Often microemulsions can form spontaneously when their components are brought together at ambient temperature. This can be particularly advantageous when formulating thermolabile drugs, peptides or iRNAs. Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications. It is expected that the microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of iRNAs and nucleic acids from the gastrointestinal tract, as well as improve the local cellular uptake of iRNAs and nucleic acids.

Microemulsions of the present invention can also contain additional components and additives such as sorbitan monostearate (Grill 3), Labrasol, and penetration enhancers to improve the properties of the formulation and to enhance the absorption of the iRNAs and nucleic acids of the present invention. Penetration enhancers used in the microemulsions of the present invention can be classified as belonging to one of five broad categories—surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of these classes has been discussed above.

iii. Microparticles

An RNAi agent of the invention may be incorporated into a particle, e.g., a microparticle. Microparticles can be produced by spray-drying, but may also be produced by other methods including lyophilization, evaporation, fluid bed drying, vacuum drying, or a combination of these techniques.

iv. Penetration Enhancers

In one embodiment, the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly iRNAs, to the skin of animals. Most drugs are present in solution in both ionized and nonionized forms. However, usually only lipid soluble or lipophilic drugs readily cross cell membranes. It has been discovered that even non-lipophilic drugs can cross cell membranes if the membrane to be crossed is treated with a penetration enhancer. In addition to aiding the diffusion of non-lipophilic drugs across cell membranes, penetration enhancers also enhance the permeability of lipophilic drugs.

Penetration enhancers can be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (see e.g., Malmsten, M. Surfactants and polymers in drug delivery, Informa Health Care, New York, NY, 2002; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of the above mentioned classes of penetration enhancers are described below in greater detail.

Surfactants (or “surface-active agents”) are chemical entities which, when dissolved in an aqueous solution, reduce the surface tension of the solution or the interfacial tension between the aqueous solution and another liquid, with the result that absorption of iRNAs through the mucosa is enhanced. In addition to bile salts and fatty acids, these penetration enhancers include, for example, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether) (see e.g., Malmsten, M. Surfactants and polymers in drug delivery, Informa Health Care, New York, NY, 2002; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92); and perfluorochemical emulsions, such as FC-43. Takahashi et al., J. Pharm. Pharmacol., 1988, 40, 252).

Various fatty acids and their derivatives which act as penetration enhancers include, for example, oleic acid, lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein (1-monooleoyl-rac-glycerol), dilaurin, caprylic acid, arachidonic acid, glycerol 1-monocaprate, 1-dodecylazacycloheptan-2-one, acylcarnitines, acylcholines, C₁₋₂₀ alkyl esters thereof (e.g., methyl, isopropyl and t-butyl), and mono- and di-glycerides thereof (i.e., oleate, laurate, caprate, myristate, palmitate, stearate, linoleate, etc.) (see e.g., Touitou, E., et al. Enhancement in Drug Delivery, CRC Press, Danvers, M A, 2006; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm. Pharmacol., 1992, 44, 651-654).

The physiological role of bile includes the facilitation of dispersion and absorption of lipids and fat-soluble vitamins (see e.g., Malmsten, M. Surfactants and polymers in drug delivery, Informa Health Care, New York, NY, 2002; Brunton, Chapter 38 in: Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al. Eds., McGraw-Hill, New York, 1996, pp. 934-935). Various natural bile salts, and their synthetic derivatives, act as penetration enhancers. Thus the term “bile salts” includes any of the naturally occurring components of bile as well as any of their synthetic derivatives. Suitable bile salts include, for example, cholic acid (or its pharmaceutically acceptable sodium salt, sodium cholate), dehydrocholic acid (sodium dehydrocholate), deoxycholic acid (sodium deoxycholate), glucholic acid (sodium glucholate), glycholic acid (sodium glycocholate), glycodeoxycholic acid (sodium glycodeoxycholate), taurocholic acid (sodium taurocholate), taurodeoxycholic acid (sodium taurodeoxycholate), chenodeoxycholic acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA), sodium tauro-24,25-dihydro-fusidate (STDHF), sodium glycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (see e.g., Malmsten, M. Surfactants and polymers in drug delivery, Informa Health Care, New York, NY, 2002; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Swinyard, Chapter 39 In: Remington's Pharmaceutical Sciences, 18th Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990, pages 782-783; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharm. Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm. Sci., 1990, 79, 579-583).

Chelating agents, as used in connection with the present invention, can be defined as compounds that remove metallic ions from solution by forming complexes therewith, with the result that absorption of iRNAs through the mucosa is enhanced. With regards to their use as penetration enhancers in the present invention, chelating agents have the added advantage of also serving as DNase inhibitors, as most characterized DNA nucleases require a divalent metal ion for catalysis and are thus inhibited by chelating agents (Jarrett, J. Chromatogr., 1993, 618, 315-339). Suitable chelating agents include but are not limited to disodium ethylenediaminetetraacetate (EDTA), citric acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate and homovanilate), N-acyl derivatives of collagen, laureth-9 and N-amino acyl derivatives of beta-diketones (enamines)(see e.g., Katdare, A. et al., Excipient development for pharmaceutical, biotechnology, and drug delivery, CRC Press, Danvers, M A, 2006; Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Buur et al., J. Control Rel., 1990, 14, 43-51).

As used herein, non-chelating non-surfactant penetration enhancing compounds can be defined as compounds that demonstrate insignificant activity as chelating agents or as surfactants but that nonetheless enhance absorption of iRNAs through the alimentary mucosa (see e.g., Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33). This class of penetration enhancers includes, for example, unsaturated cyclic ureas, 1-alkyl- and 1-alkenylazacyclo-alkanone derivatives (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92); and non-steroidal anti-inflammatory agents such as diclofenac sodium, indomethacin and phenylbutazone (Yamashita et al., J. Pharm. Pharmacol., 1987, 39, 621-626).

Agents that enhance uptake of iRNAs at the cellular level can also be added to the pharmaceutical and other compositions of the present invention. For example, cationic lipids, such as lipofectin (Junichi et al, U.S. Pat. No. 5,705,188), cationic glycerol derivatives, and polycationic molecules, such as polylysine (Lollo et al., PCT Application WO 97/30731), are also known to enhance the cellular uptake of dsRNAs. Examples of commercially available transfection reagents include, for example Lipofectamine™ (Invitrogen; Carlsbad, CA), Lipofectamine 2000™ (Invitrogen; Carlsbad, CA), 293fectin™ (Invitrogen; Carlsbad, CA), Cellfectin™ (Invitrogen; Carlsbad, CA), DMRIE-C™ (Invitrogen; Carlsbad, CA), FreeStyle™ MAX (Invitrogen; Carlsbad, CA), Lipofectamine™ 2000 CD (Invitrogen; Carlsbad, CA), Lipofectamine™ (Invitrogen; Carlsbad, CA), RNAiMAX (Invitrogen; Carlsbad, CA), Oligofectamine™ (Invitrogen; Carlsbad, CA), Optifect™ (Invitrogen; Carlsbad, CA), X-tremeGENE Q2 Transfection Reagent (Roche; Grenzacherstrasse, Switzerland), DOTAP Liposomal Transfection Reagent (Grenzacherstrasse, Switzerland), DOSPER Liposomal Transfection Reagent (Grenzacherstrasse, Switzerland), or Fugene (Grenzacherstrasse, Switzerland), Transfectam® Reagent (Promega; Madison, WI), TransFast™ Transfection Reagent (Promega; Madison, WI), Tfx™-20 Reagent (Promega; Madison, WI), Tfx™-50 Reagent (Promega; Madison, WI), DreamFect™ (OZ Biosciences; Marseille, France), EcoTransfect (OZ Biosciences; Marseille, France), TransPass^(a) D1 Transfection Reagent (New England Biolabs; Ipswich, MA, USA), LyoVec™/LipoGen™ (Invitrogen; San Diego, CA, USA), PerFectin Transfection Reagent (Genlantis; San Diego, CA, USA), NeuroPORTER Transfection Reagent (Genlantis; San Diego, CA, USA), GenePORTER Transfection reagent (Genlantis; San Diego, CA, USA), GenePORTER 2 Transfection reagent (Genlantis; San Diego, CA, USA), Cytofectin Transfection Reagent (Genlantis; San Diego, CA, USA), BaculoPORTER Transfection Reagent (Genlantis; San Diego, CA, USA), TroganPORTER™ transfection Reagent (Genlantis; San Diego, CA, USA), RiboFect (Bioline; Taunton, MA, USA), PlasFect (Bioline; Taunton, MA, USA), UniFECTOR (B-Bridge International; Mountain View, CA, USA), SureFECTOR (B-Bridge International; Mountain View, CA, USA), or HiFect™ (B-Bridge International, Mountain View, CA, USA), among others.

Other agents can be utilized to enhance the penetration of the administered nucleic acids, including glycols such as ethylene glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and terpenes such as limonene and menthone.

v. Carriers

Certain compositions of the present invention also incorporate carrier compounds in the formulation. As used herein, “carrier compound” or “carrier” can refer to a nucleic acid, or analog thereof, which is inert (i.e., does not possess biological activity per se) but is recognized as a nucleic acid by in vivo processes that reduce the bioavailability of a nucleic acid having biological activity by, for example, degrading the biologically active nucleic acid or promoting its removal from circulation. The coadministration of a nucleic acid and a carrier compound, typically with an excess of the latter substance, can result in a substantial reduction of the amount of nucleic acid recovered in the liver, kidney or other extracirculatory reservoirs, presumably due to competition between the carrier compound and the nucleic acid for a common receptor. For example, the recovery of a partially phosphorothioate dsRNA in hepatic tissue can be reduced when it is coadministered with polyinosinic acid, dextran sulfate, polycytidic acid or 4-acetamido-4′isothiocyano-stilbene-2,2′-disulfonic acid (Miyao et al., DsRNA Res. Dev., 1995, 5, 115-121; Takakura et al., DsRNA & Nucl. Acid Drug Dev., 1996, 6, 177-183.

vi. Excipients

In contrast to a carrier compound, a “pharmaceutical carrier” or “excipient” is a pharmaceutically acceptable solvent, suspending agent or any other pharmacologically inert vehicle for delivering one or more nucleic acids to an animal. The excipient can be liquid or solid and is selected, with the planned manner of administration in mind, so as to provide for the desired bulk, consistency, etc., when combined with a nucleic acid and the other components of a given pharmaceutical composition. Typical pharmaceutical carriers include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calcium hydrogen phosphate, etc.); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, corn starch, polyethylene glycols, sodium benzoate, sodium acetate, etc.); disintegrants (e.g., starch, sodium starch glycolate, etc.); and wetting agents (e.g., sodium lauryl sulphate, etc).

Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can also be used to formulate the compositions of the present invention. Suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

Formulations for topical administration of nucleic acids can include sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the nucleic acids in liquid or solid oil bases. The solutions can also contain buffers, diluents and other suitable additives. Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can be used.

Suitable pharmaceutically acceptable excipients include, but are not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

vii. Other Components

The compositions of the present invention can additionally contain other adjunct components conventionally found in pharmaceutical compositions, at their art-established usage levels. Thus, for example, the compositions can contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or can contain additional materials useful in physically formulating various dosage forms of the compositions of the present invention, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. However, such materials, when added, should not unduly interfere with the biological activities of the components of the compositions of the present invention. The formulations can be sterilized and, if desired, mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously interact with the nucleic acid(s) of the formulation.

Aqueous suspensions can contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension can also contain stabilizers.

In some embodiments, pharmaceutical compositions featured in the invention include (a) one or more iRNA compounds and (b) one or more agents which function by a non-RNAi mechanism and which are useful in treating, e.g., PH1.

Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds that exhibit high therapeutic indices are preferred.

The data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of compositions featured herein in the invention lies generally within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage can vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the methods featured in the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range of the compound or, when appropriate, of the polypeptide product of a target sequence (e.g., achieving a decreased concentration of the polypeptide) that includes the IC₅₀ (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma can be measured, for example, by high performance liquid chromatography.

In addition to their administration, as discussed above, the iRNAs featured in the invention can be administered in combination with other known agents effective in treatment of pathological processes that are mediated by iron overload and that can be treated by inhibiting HAO1 expression. In any event, the administering physician can adjust the amount and timing of iRNA administration on the basis of results observed using standard measures of efficacy known in the art or described herein.

VII. Kits

The present invention also provides kits for performing any of the methods of the invention. Such kits include one or more dsRNA agent(s) and instructions for use, e.g., instructions for administering a prophylactically or therapeutically effective amount of a double stranded RNAi agent(s). The double stranded RNAi agent may be in a vial or a pre-filled syringe. The kits may optionally further comprise means for administering the double stranded RNAi agent (e.g., an injection device, such as a pre-filled syringe), or means for measuring the inhibition of HAO1 (e.g., means for measuring the inhibition of HAO1 mRNA, HAO1 protein, and/or HAO1 activity). Such means for measuring the inhibition of HAO1 may comprise a means for obtaining a sample from a subject, such as, e.g., a plasma sample. The kits of the invention may optionally further comprise means for determining the therapeutically effective or prophylactically effective amount.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the iRNAs and methods featured in the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

This invention is further illustrated by the following examples which should not be construed as limiting. The entire contents of all references, patents and published patent applications cited throughout this application, as well as the informal Sequence Listing and Figures, are hereby incorporated herein by reference.

EXAMPLES Materials and Methods

The following materials and methods were used in the Examples. As used herein, “HAO,” “HAO1,” “GO1,” and “GO” are used interchangeably.

siRNA Synthesis

Single-stranded RNAs were produced by solid phase synthesis on a scale of 1 μmole using an Expedite 8909 synthesizer (Applied Biosystems, Applera Deutschland GmbH, Darm-stadt, Germany) and controlled pore glass (CPG, 500 Å, Proligo Biochemie GmbH, Hamburg, Germany) as solid support. RNA and RNA containing 2′-O-methyl nucleotides were generated by solid phase synthesis employing the corresponding phosphoramidites and 2′-O-methyl phos-phoramidites, respectively (Proligo Biochemie GmbH, Hamburg, Germany). These building blocks were incorporated at selected sites within the sequence of the oligoribonucleotide chain using standard nucleoside phosphoramidite chemistry such as described in Current protocols in nucleic acid chemistry, Beaucage, S. L. et al. (Edrs.), John Wiley & Sons, Inc., New York, NY, USA. Phosphorothioate linkages were introduced by replacement of the iodine oxidizer solution with a solution of the Beaucage reagent (Chruachem Ltd, Glasgow, UK) in acetonitrile (1%). Further ancillary reagents were obtained from Mallinckrodt Baker (Griesheim, Germany).

Deprotection and purification of the crude oligoribonucleotides by anion exchange HPLC were carried out according to established procedures. Yields and concentrations were determined by UV absorption of a solution of the respective RNA at a wavelength of 260 nm using a spectral photometer (DU 640B, Beckman Coulter GmbH, Unterschleißheim, Germany).

Double stranded RNA was generated by mixing an equimolar solution of complementary strands in annealing buffer (20 mM sodium phosphate, pH 6.8; 100 mM sodium chloride), heated in a water bath at 85-90° C. for 3 minutes and cooled to room temperature over a period of 3-4 hours. The annealed RNA solution was stored at −20° C. until use.

In some instances, a duplex (dsRNA) was synthesized more than once. Different batches are labeled with different extensions. For example, AD-62933.1 and AD-62933.2 are different batches of the same duplex.

Cell Culture and Transfections

Primary Cynomolgus monkey hepatocytes (PCH) and primary mouse hepatocytes (PMH) were used. PCHs (Celsis #M003055, lot CBT) or PMH (freshly isolated) were transfected by adding 14.8 μl of Opti-MEM plus 0.2 μl of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad CA. cat #13778-150) to 5 μl of siRNA duplexes per well into a 96-well plate and incubated at room temperature for 15 minutes. 80 μl of InVitroGRO CP Rat media (InVitro Technologies) containing ˜2×10⁴ PCH or PMH cells were then added to the siRNA mixture. Cells were incubated for 24 hours prior to RNA purification. Single dose experiments were performed at 10 or 20 nM and 0.1 or 0.2 nM final duplex concentration and dose response experiments were done over a range of doses from 10 nM to 36 fM final duplex concentration over 8, 6-fold dilutions.

Total RNA Isolation

Total RNA was isolated using DYNABEADS mRNA Isolation Kit (Invitrogen, part #: 610-12). Cells were harvested and lysed in 150 μl of Lysis/Binding Buffer then mixed for 5 minute at 850 rpm using an Eppendorf Thermomixer (the mixing speed was the same throughout the process). Ten microliters of magnetic beads and 80 μl Lysis/Binding Buffer mixture were added to a round bottom plate and mixed for 1 minute. Magnetic beads were captured using magnetic stand and the supernatant was removed without disturbing the beads. After removing supernatant, the lysed cells were added to the remaining beads and mixed for 5 minutes. After removing supernatant, magnetic beads were washed 2 times with 150 μl Wash Buffer A and mixed for 1 minute. Beads were capture again and supernatant removed. Beads were then washed with 150 μl Wash Buffer B, captured and supernatant was removed. Beads were next washed with 150 μl Elution Buffer, captured and supernatant removed. Beads were allowed to dry for 2 minutes. After drying, 50 μl of Elution Buffer was added and mixed for 5 minutes at 70° C. Beads were captured on magnet for 5 minutes. 40 μl of supernatant was removed and added to another 96 well plate.

cDNA synthesis

Synthesis of cDNA was performed using the ABI High capacity cDNA reverse transcription kit (Applied Biosystems, Foster City, CA, Cat #4368813).

A master mix of 2 μl 10× Buffer, 0.8 μl 25× dNTPs, 2 μl Random primers, 1 μl Reverse Transcriptase, 1 μl RNase inhibitor and 3.2 μl of H2O per reaction were added into 10 μl total RNA. cDNA was generated using a Bio-Rad C-1000 or S-1000 thermal cycler (Hercules, CA) through the following steps: 25° C. 10 min, 37° C. 120 min, 85° C. 5 sec, 4° C. hold.

Real time PCR

2 μl of cDNA were added to a master mix containing 0.5 μl of mouse GAPDH (cat #4352339E Life Technologies) or custom designed Cynomolgus monkey GAPDH TaqMan Probes: (F-GCATCCTGGGCTACACTGA, (SEQ ID NO: 7) R-TGGGTGTCGCTGTTGAAGTC (SEQ ID NO: 8), Probe-CCAGGTGGTCTCCTCC (SEQ ID NO: 9)), 0.5 μl human or mouse HAO1 (HS00213909_M1-which is cross reactive with Cynomolgus monkey HOA1, Mm 00439249_m1 for mouse assays, life technologies) and 5 μl Lightcycler 480 probe master mix (Roche Cat #04887301001) per well in a 384 well 50 plates (Roche cat #04887301001). Real time PCR was done in a LightCycler480 Real Time PCR system (Roche) using the ΔΔCt(RQ) assay. Each duplex was tested in two independent transfections and each transfection was assayed in duplicate, unless otherwise noted in the summary tables.

To calculate relative fold change, real time data were analyzed using the ΔΔCt method and normalized to assays performed with cells transfected with 10 nM AD-1955, or mock transfected cells. IC50s were calculated using a 4 parameter fit model using XLFit and normalized to cells transfected with AD-1955 or naïve cells.

The sense and antisense sequences of AD-1955 are: SENSE: 5′-cuuAcGcuGAGuAcuucGAdTsdT-3′ (SEQ ID NO: 10); and ANTISENSE: 5′-UCGAAGuACUcAGCGuAAGdTsdT-3′ (SEQ ID NO: 11).

TABLE B Abbreviations of nucleotide monomers used in nucleic acid sequence representation. Abbreviation Nucleotide(s) A Adenosine-3′-phosphate Ab beta-L-adenosine-3-phosphate Af 2′-fluoroadenosine-3′-phosphate Afs 2′-fluoroadenosine-3′-phosphorothioate As adenosine-3′-phosphorothioate C cytidine-3′-phosphate Cb beta-L-cytidine-3′-phosphate Cf 2′-fluorocytidine-3′-phosphate Cfs 2′-fluorocytidine-3′-phosphorothioate Cs cytidine-3′-phosphorothioate G guanosine-3′-phosphate Gb beta-L-guanosine-3′-phosphate Gbs beta-L-guanosine-3-phosphorothioate Gf 2′-fluoroguanosine-3′-phosphate Gfs 2′-fluoroguanosine-3′-phosphorothioate Gs guanosine-3′-phosphorothioate T 5′-methyluridine-3′-phosphate Tf 2′-fluoro-5-methyluridine-3′-phosphate Tfs 2′-fluoro-5-methyluridine-3′-phosphorothioate Ts 5-methyluridine-3′-phosphorothioate U Uridine-3′-phosphate Uf 2′-fluorouridine-3′-phosphate Ufs 2′-fluorouridine-3′-phosphorothioate Us uridine-3′-phosphorothioate N any nucleotide (G, A, C, T or U) a 2′-O-methyladenosine-3′-phosphate as 2′-O-methyladenosine-3′-phosphorothioate C 2′-O-methylcytidine-3′-phosphate CS 2′-O-methylcytidine-3′-phosphorothioate g 2′-O-methylguanosine-3′-phosphate gs 2′-O-methylguanosine-3′-phosphorothioate t 2′-O-methyl-5-methyluridine-3′-phosphate ts 2′-O-methyl-5-methyluridine-3′-phosphorothioate u 2′-O-methyluridine-3′-phosphate us 2′-O-methyluridine-3′-phosphorothioate dT 2′-deoxythymidine dTs 2′-deoxythymidine-3′-phosphorothioate dU 2′-deoxyuridine s phosphorothioate linkage L96 N-[tris(GalNAc-alkyl)-amidodecanoyl)]-4-hydroxyprolinol Hyp-(GalNAc-alkyl)3

(Aeo) 2′-O-methoxyethyladenosine-3′-phosphate (Aeos) 2′-O-methoxyethyladenosine-3′-phosphorothioate (Geo) 2′-O-methoxyethylguanosine-3′-phosphate (Geos) 2′-O-methoxyethylguanosine-3′-phosphorothioate (Teo) 2′-O-methoxyethyl-5-methyluridine-3′-phosphate (Teos) 2′-O-methoxyethyl-5-methyluridine-3′-phosphorothioate (m5Ceo) 2′-O-methoxyethyl-5-methylcytidine-3′-phosphate (m5Ceos) 2′-O-methoxyethyl-5-methylcytidine-3′-phosphorothioate (A3m) 3′-O-methyladenosine-2-phosphate (A3mx) 3′-O-methyl-xylofuranosyladenosine-2′-phosphate (G3m) 3′-O-methylguanosine-2-phosphate (G3mx) 3′-O-methyl-xylofuranosylguanosine-2′-phosphate (C3m) 3′-O-methylcytidine-2-phosphate (C3mx) 3′-O-methyl-xylofuranosylcytidine-2′-phosphate (U3m) 3′-O-methyluridine-2-phosphate (U3mx) 3′-O-methylxylouridine-2′-phosphate (Chd) 2′-O-hexadecyl-cytidine-3′-phosphate (pshe) Hydroxyethylphosphorothioate (Uhd) 2′-O-hexadecyl-uridine-3′-phosphate (Tgn) Thymidine-glycol nucleic acid (GNA) S-Isomer (Cgn) Cytidine-glycol nucleic acid (GNA) (Chd) 2′-O-hexadecyl-cytidine-3′-phosphate (Ggn) 2′-O-hexadecyl-cytidine-3′-phosphate (Agn) Adenosine-glycol nucleic acid (GNA) P 5′-phosphate (m5Cam) 2′-O-(N-methylacetamide)-5-methylcytidine-3-phosphate (m5Cams) 2′-O-(N-methylacetamide)-5-methylcytidine-3-phosphorothioate (Tam) 2′-O-(N-methylacetamide)thymidine-3-phosphate (Tams) 2′-O-(N-methylacetamide)thymidine-3-phosphorothioate (Aam) 2′-O-(N-methylacetamide)adenosine-3-phosphate (Aams) 2′-O-(N-methylacetamide)adenosine-3-phosphorothioate (Gam) 2′-O-(N-methylacetamide)guanosine-3-phosphate (Gams) 2′-O-(N-methylacetamide)guanosine-3-phosphorothioate Y34 abasic 2′-O-Methyl Y44 2-hydroxymethyl-tetrahydrofurane-5-phosphate

Example 1: ALN-65585

AD-65585 is a double stranded siRNA targeting nucleotides 1341-1363 of the human HAO1 gene. “ALN-GO1” refers to the modified, GalNAc version of AD-65585, also referred to as Lumasiran. Abbreviations of nucleotide monomers are as in Table B.

The sequence of each strand is as follows:

SEQ   ID Sequence Duplex NO 5′-3′ Strand AD-65585 12 GACUUUCAUCCUGGAAAUAUA Sense unmodified AD-65585 13 UAUAUUUCCAGGAUGAAAGUCCA Anti- unmodified sense AD-65585  14 gsascuuuCfaUfCfCfuggaaa Sense modified uauaL96 AD-65585  15 usAfsuauUfuCfCfaggaUfgA Anti- modified faagucscsa sense

Example 2: Pharmacology Studies with ALN-65585

HAO1 Inhibition in Hepatocytes.

Primary cyno hepatocytes were transfected with RNAimax (Invitrogen) with serially diluted AD-65585 (ALN-65585, “ALN-GO1”) or a non-targeting mRNA Luciferase control (AD1955) at 10 nM. Relative levels of HAO1 mRNA were determined by normalizing to GAPDH mRNA levels as quantified by real-time RT-PCR. The data was plotted to calculate the IC₅₀ value of 10 pM. The results are shown FIG. 3 .

In vitro transfection of AD-65585 demonstrates an ED₅₀ of approximately 10 pM in primary cynomolgus hepatocytes.

Single Dose Pharmacology in Mouse

ALN-GO1 pharmacology was evaluated in mice by quantifying liver HAO1 mRNA and serum glycolate levels (FIG. 4 ). A single SC dose of ALN-GO1 resulted in a dose dependent suppression of HAO1 mRNA with a dose of 10 mg/kg resulting in ED₉₀ silencing. The ED dose for GO1 silencing in the mouse was estimated to be 0.3 mg/kg. Serum glycolate levels increased in a dose-responsive manner with a maximum level approximately 4-fold above baseline levels. The results are shown in FIG. 4 , illustrating levels of liver HAO1 mRNA and serum glycolate 10 days after a single subcutaneous dose of ALN-65585 in C57BL/6 mice. Bars represent the mean of 3 or 4 animals and error bars depict the standard deviation.

Single Dose Duration in Mouse

GO1 silencing was durable and reversible post a single SC dose (FIG. 5 ). A single SC dose of ALN-GO1 in mice at 3 mg/kg resulted in ≥70% mRNA silencing for approximately 6 weeks, after which mRNA levels recovered to baseline levels through 12 weeks post-dose. The results are shown in FIG. 5 : Levels of liver HAO1 mRNA at multiple time points following a single subcutaneous dose of ALN-65585 in C57BL/6 mice. Each data point represents the mean of 3 animals and error bars depict the standard deviation.

Single Dose Pharmacology in Rat

ALN-GO1 pharmacology was also evaluated in rats by quantifying liver HAO1 mRNA levels (FIG. 6 ). A single SC administration of ALN-GO1 to male Sprague Dawley rats resulted in a dose dependent suppression of HAO1 mRNA with a dose of ≥3 mg/kg resulting in ED90 silencing. The results are shown in FIG. 6 : Levels of liver HAO1 mRNA 10 days after a single subcutaneous dose of ALN-65585 in Sprague Dawley rats. Bars represent the mean of 3 animals and error bars depict the standard deviation. The ED50 dose for GO1 silencing in the rat was estimated to be 0.3 mg/kg.

Single Dose Pharmacology in AGXT KO Mouse

The impact of ALN-GO1 on oxalate levels was evaluated in an AGXT KO mouse model of PH1. The results are shown in FIG. 7 : 24 hr urinary oxalate (top) and glycolate (bottom) excretion of Agxt KO mice after a single subcutaneous dose of ALN-65585. Different letters means significant difference between the 3 dose groups at each specific week (n=3 per dose). Urinary excretions over time did not change significantly in the PBS control animal (n=1).

Urinary oxalate levels showed dose-dependent reductions after a single dose of ALN-GO1 with a maximum of approximately 50% oxalate lowering at the 3 mg/kg dose that lasted for ≥3 weeks before recovery to pre-dose levels. Urinary glycolate levels showed dose-dependent increases after a single dose of ALN-GO1 with a maximum of approximately 5-fold increases at the 3 mg/kg dose that lasted for ≥4 weeks.

Single Dose Pharmacology in PH1 Induced Rat Model

ALN-GO1 was evaluated in a second PH1 rodent model where liver AGXT was inhibited in rats using siRNA and oxalate levels were stimulated with ethylene glycol (FIG. 8A and FIG. 8B). Liver HAO1 mRNA and 24-hour urinary oxalate were quantified to determine the degree of HAO1 lowering required for maximal oxalate reduction. The results are shown in FIG. 8A and FIG. 8B: Levels of liver HAO1 mRNA a rat induced model of PH1 14 days after a single subcutaneous dose of ALN-65585 and weekly dosing of AF-011-AGXT siRNA (2 doses, of 1 mg/kg). 24 hr urinary oxalate normalized to urinary creatinine. Bars represent the mean of 3 animals and error bars depict the standard deviation. mRNA and oxalate lowering correlation plot represents individual animals from multiple experiments.

A single dose of ALN-GO1 in this model demonstrated dose-responsive mRNA and urinary oxalate lowering with approximately 85% maximum mRNA reduction and approximately 90% maximum urinary oxalate reduction observed at the highest dose of ALN-GO1 (FIG. 8A and FIG. 8B). In this induced rat model of PH1, mRNA and urinary oxalate reductions resulted in a 1:1 correlation.

Multi-Dose Pharmacology in PH1 Induced Rat Model

Potency of ALN-GO1 was evaluated in studies in normal rats with inhibited AGXT activity and ethylene glycol (an induced model of PH1) by quantifying liver HAO1 mRNA and 24-hour urinary oxalate. The results are shown in FIG. 9 : Levels of liver HAO1 mRNA a rat induced model of PH1 28 days after repeat subcutaneous dosing of ALN-65585 and repeat IV dosing of AF-011-AGXT siRNA (4 doses, of 1 mg/kg). 24 hr urinary oxalate normalized to urinary creatinine. Bars represent the mean of 2 or 3 animals and error bars depict the standard deviation.

Treatment with ALN-GO1 resulted in sustained urinary oxalate reductions in all treatment groups for approximately 3 weeks. On day 28 after repeat dosing of ALN-GO1 (and four doses of AF-011-AGXT) all groups showed >95% mRNA reduction >85% urinary oxalate lowering.

Multi-Dose Pharmacology in NHP

ALN-GO1 pharmacology was evaluated in cynomolgus monkeys (non-human primate (NHP)) by quantifying HAO1 mRNA in liver biopsy, and serum glycolate levels. The following table shows the NHP Pharmacology study outline detailing dose level and dose regimen.

Group # Test Article Dose level (mg/kg) Dose frequency 1 PBS Na QM x 6 2 AD-65585 0.25 QM x 8 3 AD-65585 1 QM x 8 4 AD-65585 1 QM x 6 5 AD-65585 2 QM x 6 6 AD-65585 4 QM x 6 7 AD-65585 2 −> 1 QM x 4 −> QM x 5

The results are shown in FIG. 10 . NHP serum glycolate levels for all groups out to day 85, data represents group averages of 3 animals per group, lines represent standard deviation. Liver biopsy HAO1 mRNA on Day 29, lines represent group averages, symbols represent individual animal mRNA levels relative to PBS control on Day 29.

After the first month of dosing (day 29), dose-responsive mRNA silencing was observed in all groups, with up to 99% mRNA silencing in groups 6 and 7 dosed with 4 mg/kg monthly or 2 mg/kg weekly. Maximum elevated serum glycolate levels of approximately 70 M were maintained for at least 3 weeks in group 6 dosed with 4 mg/kg monthly.

Example 3: ALN-GO1 Phase 1/2 Study in Human Subjects

A single ascending dose (SAD) study was performed in 32 healthy adult volunteer human subjects using AD-65585 (ALN-65585, “ALN-GO1”) or a placebo administered subcutaneously. The dosing schedule was as follows:

0.3 mg/kg×1 SC, N=8

1.0 mg/kg×1 SC, N=8

3.0 mg/kg×1 SC, N=8

6.0 mg/kg×1 SC, N=8

Safety, pharmacokinetics, and pharmacodynamics were evaluated. No serious adverse events or discontinuations due to adverse events occurred. No other clinically significant changes in liver function, kidney function, or blood parameters were observed.

Serum glycolate levels were determined using methods described herein and/or well known to one of skill in the art. The results are shown in FIG. 11 and FIG. 12 . Serum glycolate levels increased in a dose-dependent manner with earliest onset of activity at higher doses evident by Day 29 post dose and sustained until Day 85. The lowest dose with appreciable glycolate increase was 1 mg/kg.

The results demonstrate a method of increasing a plasma glycolate level in a subject, the method comprising administering to the subject an effective amount of a ALN-GO1 siRNA, thereby increasing plasma glycolate levels in the subject. The effective amount can be 1.0, 3.0, or 6.0 mg/kg. The ALN-GO1 siRNA can be administered subcutaneously.

Example 4: ALN-GO1 Phase 1/2 Study in Patients with PH1

A multiple ascending dose (MAD) study was performed on PH1 patients using Lumasiran, e.g., AD-65585 (ALN-65585, “ALN-GO1”) or a placebo administered subcutaneously in a randomized 3:1, single blind, placebo controlled study.

The dosing schedule was as follows:

1.0 mg/kg, q28d×3 SC, N=4

3.0 mg/kg, q28d×3 SC, N=4

3.0 mg/kg, q84d×2 SC, N=4

The PH1 patients ranged in age from 6-64 years; had an eGFR (estimated glomerular filtration rate) of >45 ml/min/1.73 m2; and had urinary oxalate excretion of >0.70 mmol/24 h/1.73 m².

Cohorts 1 and 2 each the following demographics:

Characteristic N = 8 Age range, years 6-19 Gender Male 5 Female 3 Race Caucasian 4 Asian 2 Arabic 1 Asian Indian 1

Safety was evaluated. No serious adverse events or discontinuations due to adverse events occurred.

Cohort 1 was administered ALN-GO1 using the following dosing schedule: 1 mg/kg q28d×3 doses. Urinary oxalate excretion levels were determined using methods described herein and/or well known to one of skill in the art. The results are shown in FIG. 13 . Administration of ALN-GO1 reduced urinary oxalate excretion by greater than 50%.

Cohort 2 was administered ALN-GO1 using the following dosing schedule: 3 mg/kg q28d×3 doses. Urinary oxalate excretion levels were determined using methods described herein and/or well known to one of skill in the art. The results are shown in FIG. 14 . After the first dose of ALN-GO1 or placebo, the mean urinary oxalate excretion at Day 29 decreased by a mean of >50%. Placebo was included in summary as patients remain blinded in the ongoing study.

For all patients, administration of ALN-GO1 lowered urinary oxalate below 1.1 mmol/1.73 m²/24 hours with baseline excretion ≥1.6 mmol/1.73 m²/24 hours. It has been shown that among patients with PH who did not have ESRD at diagnosis, renal survival estimates were lower in those with the highest level of urinary oxalate excretion (Zhao et al. CJASN 2016; 11:119-126).

The study demonstrates that multiple doses of AD-65585 (ALN-65585, “ALN-GO1”) are well tolerated by patients with PH1 with no drug related SAEs or discontinuations from study. The drug treatment achieved substantial reductions in urinary oxalate levels in all patients treated, highlighting the potential of substrate reduction therapy through RNAi-mediated glycolate oxidase inhibition.

Initial Results Part B: ALN-GO1 Phase 1/2 Study in Patients with PH1

Part B is a randomized (3:1 drug:placebo), single-blind, placebo-controlled evaluation of lumasiran in patients with PH1. Cohorts 1 and 2 received three monthly doses of lumasiran (ALN-65585, “ALN-GO1”) at 1 mg/kg or 3 mg/kg, respectively; cohort 3 received two quarterly doses at 3 mg/kg. An additional eight patients received open-label lumasiran in expansions of each of the first two cohorts, totaling 20 patients enrolled. Patients randomized to the placebo group also received subsequent subcutaneous administration of lumasiran following administration of placebo. Patients had a mean age of 14.9 years (range: 6-43) and a mean estimated glomerular filtration rate (eGFR) of 77 mL/min/1.73 m² (range: 42-131).

Inclusion criteria were the following: PH1; Ages 6-64 years; eGFR >45 ml/min/1.73 m²; Urinary oxalate excretion ≥0.70 mmol/24 h/1.73 m². Patient demographics were as follows:

Characteristic Result (N = 20) Mean age, years (range) 14.9 (6-43) Age <18 years 80% Gender, females 65% Mean weight, kg (range) 49.9 (21.3-111.0) Mean eGFR, mL/min/1.73 m2 (range) 77 (42-131)

RESULTS: Lumasiran demonstrated a mean maximal reduction in urinary oxalate of 65 percent in patients enrolled in Cohorts 1-3 (N=12), with all of these patients experiencing a lowering in urinary oxalate below 0.7 mmol/24 hrs/1.73 m², a threshold associated with a slower rate of progression to end-stage renal disease (data not shown). On day 85, patients receiving lumasiran with available data (N=9) maintained a mean reduction in urinary oxalate of 63 percent (range: 49-73 percent).

As shown in FIG. 15 and FIG. 16 , Lumasiran lowered UOx (urinary oxalate) below 1.1 mmol/24 hr/1.73 m² in all patients with baseline excretion ≥1.6 mmol/24 hr/1.73 m². Renal survival was examined by quartile of urine oxalate (UOx) excretion (mmol/24 hr/1.73 m²) at diagnosis. Among patients with PH who did not have ESRD at diagnosis, renal survival estimates were lower in those with highest level of urinary oxalate excretion.

The following inclusion criteria are also used. Treatment in younger patients includes birth to <6 years; eGFR >45 mL/min/1.73 m² if 12 months or older; without impaired renal function if <12 months or evidence of systemic oxalosis. Treatment in patients with advance renal disease includes all ages, and eGFR ≤45 mL/min/1.73 m² if 12 months or older, impaired renal function if <12 months OR clinical evidence of systemic oxalosis.

Lumasiran (ALN-GO1) is a subcutaneously administered investigational RNAi therapeutic that reduces hepatic production of oxalate in patients with Primary Hyperoxaluria Type 1 (PH1). Multiple doses of lumasiran have been well tolerated by patients with PH1 with no drug related SAEs or discontinuations from study. Patients receiving lumasiran experienced substantial and sustained reductions in urinary oxalate, confirming RNAi-mediated inhibition of glycolate oxidase as a robust therapeutic to alleviate pathologic overproduction of oxalate in this devastating disease. The potent and durable reductions in urinary oxalate support a once quarterly, subcutaneous dose regimen. GO inhibition reduces and normalizes levels of hepatic oxalate production, halting PH1 disease progression.

Summary of Prior Phase I/I Clinical Trials of AD-65585 (Lumasiran)

As described in the Examples above, the data from the Phase I/II clinical trials of AD-65585 (Lumasiran) demonstrated that subcutaneous administration of AD-65585 resulted in a mean maximal reduction in 24-hour urinary oxalate of 64% (Cohorts 1 to 3) and achievement of normal to near-normal levels of urinary oxalate (<0.7 mmol/24 h/1.73 m²) in patients dosed with lumasiran (range: 0.29 to 0.67 mmol/24 h/1.73 m²). This suppression of urinary oxalate was maintained with repeat dosing, indicative of the durability of the pharmacodynamic effect of lumasiran. In addition, in the multiple-ascending dose group (Part B; n=10), preliminary data showed a mean reduction of 59% in plasma oxalate relative to baseline 28 days after the last dose. The mean maximal reduction in plasma oxalate was 75% (range 57-94%), and 50% of patients achieved plasma oxalate levels within the normal range (<1.6 μmol/L).

Example 5: Pharmacokinetic-Pharmacodynamic (PK-PD) Model of ALN-GO1, an Investigational RNAi Therapeutic for Primary Hyperoxaluria 1 (PH1)

The objectives of this study were to predict ALN-GO1 liver and RISC concentration-time profiles in humans and to quantify ALN-GO1 dose response with respect to plasma glycolate elevation in healthy volunteers and urine oxalate reduction in PH1 patients.

The glycolate response profile in healthy volunteers and provided by the results from the Phase I study (described above) were adequately described by the PK-PD model, as shown in FIG. 17 . A dose dependent increase in plasma glycolate levels was observed in healthy volunteers. At a 6 mg/kg dose, a ˜6.5-fold increase in glycolate is predicted from baseline with corresponding predicted GO suppression of ˜85%.

The oxalate response in PH1 patients provided by the results from the Phase I study (described above) were adequately described by the PK-PD model, as shown in FIG. 18 . All patients treated with ALN-GO1 showed a reduction in urinary oxalate levels. After three 1 mg/kg monthly doses, peak urinary oxalate lowering is predicted to occur at 2 months post last dose followed by a slow recovery to baseline. The model predicted median maximum lowering of urinary oxalate is 56% after three 1 mg/kg monthly doses of ALN-GO1.

The PK-PD model predicted a relationship between dosage and steady-state GO enzyme inhibition in PH1 patents. As shown in FIG. 19 , monthly doses of >2 mg/kg and quarterly doses of >5 mg/kg are expected to yield >90% inhibition of GO enzyme.

The PK-PD model predicted a relationship between dosage and steady-state urine oxalate reduction in PH1 patients. As shown in FIG. 20 , monthly doses ≥2 mg/kg and quarterly doses ≥5 mg/kg are expected to yield near maximal suppression of urinary oxalate in PH1 patients. The simulations were conducted assuming median baseline urinary oxalate of 2.0 (mmol/24 h/1.73 m²).

The PK-PD model adequately described the observed time-course and inter-individual variability of plasma glycolate increase in healthy volunteers and urinary oxalate decrease in PH1 patients. A 2 mg/kg monthly or 5 mg/kg quarterly dose of ALN-GO1 can result in >90% inhibition of GO enzyme and consequently near maximal urinary oxalate reduction.

Example 6: Phase III Clinical Trial of AD-65585 and Improvement in Medullary Nephrocalcinosis

A Phase III, randomized, double-blind, placebo-controlled study was conducted to evaluate the efficacy, safety, pharmacokinetics and pharmacodynamics of subcutaneously administered AD-65585 (Lumasiran) in adults and children with confirmed primary hyperoxaluria type 1 (PH1).

The sequences of AD-65585 are described above in Example 1.

Patient population was as follows:

-   -   Adults and children ≥6 years     -   Urinary oxalate excretion ≥0.7 mmol/24 hr/1.73 m²     -   Confirmed AGXT (alanine glyoxolate amino transferase) mutations     -   eGFR ≥30 mL/min/1.73 m²

Patient population (N=39) was randomized 2:1, subject:placebo.

Lumisiran arm received a loading dose of 3.0 mg/kg Lumasiran subcutaneously once a month for 3 months, followed by a maintenance dose of 3.0 mg/kg Lumasiran subcutaneously, starting one month after the final loading dose, once every 3 months. Placebo arm received a loading dose of 3.0 mg/kg placebo subcutaneously once a month for 3 months, followed by a maintenance dose of 3.0 mg/kg Lumasiran subcutaneously, starting one month after the final loading dose, once every 3 months. The double blind treatment period lasted 6 months. All patients were followed through a 54 month extension period for a total of 60 months.

The primary outcome measure is the percentage change in urinary oxalate excretion from baseline to month 6. The secondary outcome measures include (1) percentage change in urinary oxalate excretion from baseline to end of study (month 60) (time frame: up to 60 months); (2) absolute change in urinary oxalate excretion from baseline (time frame: up to 60 months); (3) percentage of time that spot urinary oxalate:creatinine ratio ≤near-normalization threshold (≤1.5×uln) (time frame: up to 60 months); (4) percentage of participants with urinary oxalate excretion ≤the upper limit of normal (uln) and ≤1.5×uln (time frame: up to 60 months); (5) percentage change in plasma oxalate from baseline to end of study (month 60) (time frame: up to 60 months); (6) absolute change in plasma oxalate from baseline to end of study (month 60) (time frame: up to 60 months); (7) maximum observed plasma concentration (cmax) of AD-65585 (time frame: up to 24 months); (8) time to maximum observed plasma concentration (tmax) of AD-65585 (time frame: up to 24 months]; (9) elimination half-life (t½beta) of AD-65585 (time frame: up to 24 months); (10) area under the concentration-time curve (auc) of AD-65585 (time frame: up to 24 months); (11) apparent clearance (cl/f) of AD-65585 (time frame: up to 24 months); (12) apparent volume of distribution (v/f) of AD-65585 (time frame: up to 24 months); (13) change in estimated glomerular filtration rate (egfr) from baseline (time frame: up to 60 months) and (14) frequency of adverse events (aes) (time frame: up to 60 months).

Results

Reduction in 24 hr Urinary Oxalate was Sustained Through Month 12

Patients initially randomized to lumasiran (Lumasiran/Lumasiran) had a sustained reduction in 24 hr UOx through Month 12 (mean reduction from baseline 64.1%). Patients initially randomized to placebo who crossed over to lumasiran (Placebo/Lumasiran) demonstrated a similar time course and magnitude of 24 hr UOx reduction (mean reduction 57.3% after 6 months of treatment). In addition, an absolute reduction in 24 hr urinary oxalate was sustained through month 12.

Proportion of Patients that Achieved Near Normalization or Normalization of 24 hr Urinary Oxalate was Sustained Through Month 12

Lumasiran/Lumasiran patients sustained near normalization or normalization of 24 hr UOx (≤1.5×ULN) through Month 12, and 77% of Placebo/Lumasiran crossover patients achieved near normalization or normalization (≤1.5×ULN) of 24 hr UOx after 6 months of treatment.

Reduction in Plasma Oxalate was Sustained Through Month 12

Patients initially randomized to lumasiran (Lumasiran/Lumasiran) maintained their reduction in plasma oxalate through Month 12 (mean percent reduction of 35.0% at Month 12). Patients initially randomized to placebo who crossed over to lumasiran (Placebo/Lumasiran) demonstrated a similar time course and magnitude of plasma oxalate reduction. After 6 months of treatment, their plasma oxalate mean percent reduction was 48.9%.

In addition, eGFR remained stable with Lumasiran treatment through month 12. Plasma glycolate initially increased and then plateaued, consistent with reduction in hepatic GO activity.

Lower Renal Stone Event Rates after Treatment

A renal stone event was defined as an event which is patient reported and includes at least one of the following: a) a visit to healthcare provider because of a renal stone, b) medication for renal colic, c) stone passage, and/or d) macroscopic hematuria due to a renal stone. The renal stone event rate was calculated as total number of renal stone events divided by total person-years.

In the Lumasiran/Lumasiran group, renal stone event rates decreased during the first 6 months of lumasiran treatment in the patients initially randomized to lumasiran, relative to the 12 months prior to consent. This reduction was maintained after an additional 6 months of treatment, so that renal stone event rates decreased with lumasiran treatment through Month 12.

In the patients initially randomized to placebo, renal stone event rates remained unchanged during the 6 months of placebo treatment, relative to the 12 months prior to consent. After these patients crossed over from placebo to lumasiran, renal stone event rates decreased after 6 months of lumasiran treatment.

eGFR and renal stone events (reported by events per 100 person-days) were also assessed through the double-blind and extension periods for a total of 12 months. eGFR remained stable in patients administered lumasiran. In the lumasiran arm, as shown in FIG. 21A the rate of renal stone events reported 12 months prior to consent was 3.19. The observed events during the double-blind period and the first 6 months of the extension period were 1.09 and 0.85, respectively. In the placebo arm, the rate of renal stone events reported 12 months prior to consent was 0.54 and the observed events during the double-blind period were 0.66. During the first 6 months of lumasiran treatment in the extension period a rate of 0.17 events were observed in patients previously receiving placebo.

During the next six months of the extension study, study months 12-18, the rate of renal stone events in the lumasiran arm was 0.56 and in the placebo arm the rate of renal stone events was 0.0, and during months 18-24 of the study, the rate of renal stone events in the lumasiran arm was 0.63 and in the placebo arm the rate of renal stone events was 0.48.

FIG. 21B is a graph summarizing the effect of lumasiran administration on renal stone event rate by treatment period through month 24 in the lumasiran arm of the study.

Medullary Nephrocalcinosis Improvement in Patients with Lumasiran Treatment

Medullary nephrocalcinosis was assessed by renal ultrasound at baseline and Months 6, 12, and 24 centrally read by a radiologist blinded to timepoint and treatment arm. The degree of nephrocalcinosis in each kidney was graded on a standardized 4-point scale. Spontaneous improvements in medullary nephrocalcinosis are not expected in older patients with PH1 on a stable management regime. At the start of the trial, 29 patients had nephrocalcinosis at baseline—12 patients in the placebo group (92.3%) and 17 in the lumasiran group (70.8%).

For nephrocalcinosis, of the 49 patients with baseline and month 6 renal ultrasounds, 4 of 36 in the lumasiran group showed improvement in nephrocalcinosis, 1 of 36 in the lumasiran group showed worsening in nephrocalcinosis, and 1 of 13 in the placebo group showed worsening in nephrocalcinosis, as shown in FIG. 22 . None of the other lumasiran (n=36) or placebo-treated (n=13) patients exhibited a change in nephrocalcinosis after 6 months.

Of the 24 patients with baseline and month 12 renal ultrasounds in the lumasiran group, 11 of 24 showed improvement in nephrocalcinosis and 3 of 24 showed worsening in nephrocalcinosis, as shown in FIG. 22 .

At month 24 of the study, of the 13 patients in the lumasiran group with baseline and 24 month renal ultrasounds, 3 showed improvement or reduction in nephrocalcinosis, 9 showed no change in nephrocalcinosis, and 1 showed worsening or increase in nephrocalcinosis.

High levels of oxalate are toxic because oxalate cannot be broken down by the human body and accumulates in the kidneys. Oxalate can bind with calcium in the kidney, and hyperoxaluria can lead to urinary CaOx supersaturation, resulting in the formation and deposition CaOx crystals in renal tissue. These CaOx crystals may contribute to the formation of diffuse renal calcifications (nephrocalcinosis) and stones (nephrolithiasis). Moreover, when the innate renal defense mechanisms are suppressed, injury and progressive inflammation caused by these CaOx crystals, together with secondary complications such as tubular obstruction, may lead to decreased renal function and in severe cases even to end-stage renal failure. Furthermore, systemic deposition of CaOx (systemic oxalosis) may occur in extrarenal tissues, which can lead to early death if left untreated.

Example 7: Phase III Clinical Trial of AD-65585 (ILLUMINATE-B)

A Phase III, single arm, open-label study was conducted to evaluate the efficacy, safety, pharmacokinetics and pharmacodynamics of subcutaneously administered AD-65585 (Lumasiran) in infants and children with confirmed primary hyperoxaluria type 1 (PH1).

The sequences of AD-65585 are described above in Example 1.

Patient population was as follows:

-   -   Infants and children <6 years     -   Elevated urinary oxalate:creatinine ratio     -   Confirmed AGXT (alanine glyoxolate amino transferase) mutations     -   eGFR >45 mL/min/1.73 m² if ≥12 months old; normal serum         creatinine if <12 months old

Patient population (N=18).

Patients <10 kg received loading doses 6.0 mg/kg once monthly for 3 months and then maintenance doses 3.0 mg/kg once monthly; patients ≥10 to ≤20 kg received loading doses 6.0 mg/kg once monthly for 3 months and then maintenance doses 6.0 mg/kg once every 3 months; patients ≥20 kg received loading doses 3.0 mg/kg once monthly for 3 months and then maintenance doses 3.0 mg/kg once every 3 months. The maintenance dose began 1 month after the last loading dose was adminstered. The treatment period lasted 6 months. All patients are followed through a 54 month extension period for a total of 60 months.

The primary outcome measure is the percentage change in spot urinary oxalate:creatinine ratio from baseline to month 6. The secondary outcome measures include (1) percentage change in urinary oxalate excretion from baseline to end of study (month 60) (time frame: up to 60 months); (2) absolute change in urinary oxalate excretion from baseline (time frame: up to 60 months); (3) percentage of time that spot urinary oxalate:creatinine ratio ≤near-normalization threshold (≤1.5×uln) (time frame: up to 60 months); (4) percentage of participants with urinary oxalate excretion ≤the upper limit of normal (uln) and ≤1.5×uln (time frame: up to 60 months); (5) percentage change in plasma oxalate from baseline to end of study (month 60) (time frame: up to 60 months); (6) absolute change in plasma oxalate from baseline to end of study (month 60) (time frame: up to 60 months); (7) maximum observed plasma concentration (cmax) of AD-65585 (time frame: up to 24 months); (8) time to maximum observed plasma concentration (tmax) of AD-65585 (time frame: up to 24 months]; (9) elimination half-life (t½ beta) of AD-65585 (time frame: up to 24 months); (10) area under the concentration-time curve (auc) of AD-65585 (time frame: up to 24 months); (11) apparent clearance (cl/f) of AD-65585 (time frame: up to 24 months); (12) apparent volume of distribution (v/f) of AD-65585 (time frame: up to 24 months); (13) change in estimated glomerular filtration rate (egfr) from baseline (time frame: up to 60 months) and (14) frequency of adverse events (aes) (time frame: up to 60 months).

Renal stone event rates in subjects administered the weight-based dosing regimen of lumasiran described above in this Phase III, single arm, open-label study were calculated as the total number of renal stone events divided by total person-years during the respective period. The 95% CI for the event rate was obtained using a generalized linear model for a Poisson distribution unless the rate was 0, in which case the upper bound of the 95% CI was calculated using the exact Poisson method.

A renal stone event was defined as an event which includes at least one of the following: a visit to healthcare provider because of a renal stone; medication for renal colic; and/or stone passage and macroscopic hematuria due to a renal stone.

Total number of person-years was defined as: for the screening period, the duration from the date of informed consent until first lumasiran dose. For the primary analysis period, the duration from the first lumasiran dose until either the dose administration at Month 6 or the date of the Month 6 visit for patients who discontinued treatment prematurely. For the extension analysis period, the duration was by blocks of 6 months of lumasiran treatment, starting from the Month 6 lumasiran dose until the date of last exposure. For the Overall During Study period, the duration was from the first lumasiran dose until the date of last exposure. The date of last exposure was either the date of the last dose administered+84 days, the analysis cut-off date, or the end of study date (whichever is earliest).

To assess the effect of a weight-based dosing regimen described above in this Phase III, single arm, open-label study of lumasiran on medullary nephrocalcinosis, renal ultrasound was used to measure the grade of medullary nephrocalcinosis (range: 0 to 3) where a higher grade indicated greater disease severity. Changes in the grade of medullary nephrocalcinosis per kidney were categorized in 3 groups, no change; worsening; or improving. Baseline is the last assessment prior to the first dose of lumasiran. No change is the same grade as Baseline; Improving is a lower grade than Baseline; Worsening is a higher grade than Baseline. Changes in grade of nephrocalcinosis from baseline to each post-baseline visit were summarized. The distribution of patients by extent of change in nephrocalcinosis grade (i.e., number of grades by which nephrocalcinosis improved or worsened) from baseline to each post-baseline visit were also summarized. At each post-baseline visit, the number and associated percentage of patients in the following 4 categories of overall change (i.e., accounting for both kidneys), no change; improving; worsening, and indeterminate (one kidney improving and one kidney worsening) will be determined. Patients who underwent a kidney transplant were censored at the time of transplant.

Following 6 months of treatment with lumasiran, eGFR remained stable and there was no change in renal stone event rates. The low rates of kidney stone events were unchanged from 12 months prior to consent through the first 6 months of lumasiran treatment. The rate of renal stone events per person year reported 12 months prior to consent was 0.24. The observed renal stone event rate per person year during the 6 month treatment period was 0.24, as shown in FIG. 23A.

In addition, the observed renal stone event rate per person year during month 6 to month 12 of the treatment period was 0.12.

FIG. 23B summarizes the renal stone event rate per person year by treatment period.

Fifty-four percent of patients administered lumasiran showed improved nephrocalcinosis after 6 months of treatment.

Of the lumasiran-treated patients having nephrocalcinosis at baseline and for which baseline and month 6 renal ultrasounds were available, 8 of 14 patients showed improvement in nephrocalcinosis (5 showed unilateral improvement in nephrocalcinosis and 3 showed bilateral improvement in nephrocalcinosis), 6 patients showed no change in nephrocalcinosis, and 0 patients showed worsening of nephrocalcinosis over the 6 month lumasiran treatment period, as shown in FIG. 24 .

Of the 4 lumasiran-treated patients that did not have nephrocalcinosis at baseline and for which baseline and month 6 renal ultrasounds were available, none exhibited a change in nephrocalcinosis after 6 months.

At month 12 of the study, in subjects having nephrocalcinosis at baseline, 11 subjects showed a reduction in nephrrocalcinosis, 3 unilateral reduction and 8 bilateral reduction. Three patients showed no change in nephrocalcinosis and no patients exhibited a worsening of nephrocalcinosis. None of the subjects that did not have nephrocalcinosis at baseline showed any change, worsening or reduction in nephrocalcinosis at month 12 of the study.

Example 8. Phase III Clinical Trial of AD-65585 (ILLUMINATE-C)

A Phase III, single arm, open-label study was conducted to evaluate the efficacy, safety, pharmacokinetics and pharmacodynamics of subcutaneously administered AD-65585 (Lumasiran) in subjects having advanced primary hyperoxaluria type 1 (PH1), in particular, in subjects with a documented diagnosis of PH1 (confirmed by genetic analysis) who have advanced renal disease, as evident by eGFR ≤45 ml/min/1.73 m² (or serum creatinine elevated for age, in patients <12 months of age).

This study included full term infants to adults with a documented diagnosis of PH1 confirmed by genetic analysis, eGFR ≤45 mL/min/1.73 m² at screening in patients 12 months of age (in patients <12 months of age, had serum creatinine considered elevated for age), plasma oxalate ≥20 μmol/L at screening, if on pyridoxine therapy had a stable regimen for at least 90 days prior to informed consent and remained on regimen through Month 6 visit, and were willing and able to comply with all study requirements and provide informed consent (and assent, as applicable) per local and national requirements. Patients on dialysis were on hemodialysis therapy only and must had been on a stable regimen for at least 4 weeks; patients who were on hemodialysis/peritoneal dialysis combination therapy or peritoneal dialysis alone were excluded from the study.

A weight-based dose regimen was employed as follows:

Loading Dose (Day 1, Month 1, Maintenance Dose Weight Month 2) (Month 3 and Beyond) <10 kg 6.0 mg/kg monthly 3.0 mg/kg monthly, begining 1 for 3 months month after the last loading dose ≥10 to <20 kg 6.0 mg/kg monthly 6.0 mg/kg every 3 months, for 3 months begining 1 month after the last loading dose ≥20 kg 3.0 mg/kg monthly 3.0 mg/kg every 3 months, for 3 months begining 1 month after the last loading dose

The duration of treatment with lumasiran is up to 60 months, with final dose administered at the Month 57 visit. The estimated total time on study for each patient is up to 64 months, including up to 4 months of screening.

The unmodified and modified sense and antisense strand nucleotide sequences of AD-65585 are provided above in Example 1.

This study included 2 cohorts, Cohort A and Cohort B. Cohort A included patients who do not yet require dialysis. Cohort B included patients who were on dialysis therapy. Dialysis modality was restricted to patients on hemodialysis only. Cohort A patients who experienced progression of renal impairment over time and began to require dialysis therapy were crossed-over to Cohort B.

The primary outcome measure for Cohort A was the percent change in plasma oxalate from baseline to month 6.

The primary outcome measure for Cohort B was the percent change in pre-dialysis plasma oxalate from baseline to Month 6.

Secondary outcome measures for both Cohorts A and B during the primary analysis period from baseline to month 6 include percent change in plasma oxalate AUC between dialysis sessions; absolute change in plasma oxalate; change in urinary oxalate; change in quality of life (QoL) as assessed by the PedsQL Total Score for patients ≥2 to <18 years of age at consent, and as assessed by KDQOL Burden of Kidney Disease and Effect of Kidney Disease on Daily Life subscales, and SF-12 Physical Component Summary and Mental Component Summary, in patients ≥18 years at consent; and change in plasma PK parameters of lumasiran.

Secondary longterm outcome measures for both Cohorts A and B from month 6 to the end of the study (up to 60 months) include percent change in plasma oxalate AUC between dialysis sessions; percent and absolute change in plasma oxalate; change in ephrocalcinosis as assessed by renal ultrasound; change in frequency and mode of dialysis; change in frequency of renal stone events; change in urinary oxalate; change in renal function as assessed by eGFR; change in measures of systemic oxalosis in the following systems: cardiac; dermatologic; skeletal; and ocular; and change in QoL (Quality of life) assessed by the PedsQL Total Score for patients ≥2 to <18 years of age at consent, and as assessed by KDQOL Burden of Kidney Disease and Effect of Kidney Disease on Daily Life subscales, and SF-12 Physical Component Summary and Mental Component Summary, in patients ≥18 years at consent.

Exploratory outcome measures for both Cohorts A and B include growth parameters in patients who are <6 years of age at consent; change in developmental milestones over time in patients <6 years of age at consent; change in QoL as assessed by EQ-5D-Y and PedsQL (individual subscales of the generic and ESRD modules, and ESRD module total score) for patients ≥2 to 18 years of age at consent, and as assessed by EQ-5D-5L in patients ≥18 years of age at consent; change in QoL as assessed by KDQOL Symptoms and Problems of Kidney Disease subscale in patients ≥18 years of age at consent; change in patient and caregiver resource use (eg, work/school attendance, visits to doctor/hospital); change in patient and caregiver experiences as evaluated by a patient experience questionnaire and a caregiver experience questionnaire; frequency of ADA; change in urinary and plasma glycolate.

Example 9. Decreased Systemic Oxalosis in Subjects Having Primary Hyperoxaluria Following Treatment with Lumasiran

The effect of the weight-based dose regimen of lumasiran in the Phase III, single arm, open-label study described in Example 8 on cardiac systemic oxalosis was assessed by determining changes in various cardiac function parameters including left ventricular ejection fraction (LVEF), global longitudinal strain (GLS); and early mitral inflow velocity:mitral annual early diastolic velocity (E/e′) by echocardiogram (echo) for subjects in both Cohort A and Cohort B.

LVEF is the percentage of blood that is pumped out of the left ventricle with each heartbeat. A normal LVEF is about 55% to about 70%.

Left ventricular global longitudinal strain (GLS) measures the maximal shortening of myocardial longitudinal length during systole compared to the resting length in diastole. Reduced GLS may reflect abnormal systolic function before loss of ejection fraction (EF) becomes apparent. Normal values of GLS are from −15.9% to −22.1%.

Early mitral inflow velocity:mitral annual early diastolic velocity (E/e′) is a measure of left ventricle (LV) filling pressures. Normal E/e

ratio is greater than 8.

Prior to the initiation of the study at baseline (the last non-missing value collected prior to the first dose of lumasiran), the mean left ventricular ejection fraction on echo in subjects in Cohorts A and B (n=21) was 60.2 (±7.8). Following treatment, at month 6 of the study, the mean left ventricular ejection fraction on echo of subjects in Cohorts A and B (n=20) was 63.4 (±7.5), a mean change from baseline of 3.5 (±6.1), an important improvement (increase) from baseline of about >5%.

Prior to the initiation of the study at baseline (the last non-missing value collected prior to the first dose of lumasiran), the global longitudinal strain in subjects in Cohorts A and B (n=21) was −19.3 (±6.0). Following treatment, at month 6 of the study, the global longitudinal strain in subjects in Cohorts A and B (n=20) was −21.0 (±6.1), a mean change from baseline of −1.9 (±4.8), an improvement (decrease) from baseline of about >2%.

Prior to the initiation of the study at baseline (the last non-missing value collected prior to the first dose of lumasiran), the early mitral inflow velocity:mitral annual early diastolic velocity in subjects in Cohorts A and B (n=18) was 6.77 (±2.28). Following treatment, at month 6 of the study, the early mitral inflow velocity:mitral annual early diastolic velocity in subjects in Cohorts A and B (n=17) was 7.34 (±3.92), a mean change from baseline of 0.72 (±3.88), an improvement (increase) from baseline of about ≥2%.

These data demonstrate that a weight-based dosing regimen of lumasiran in subjects having primary hyperoxaluria reduces cardiac systemic oxalosis and improves cardiac function.

Example 10. Lumasiran for Patients with Primary Hyperoxaluria Type 1 with Impaired Kidney Function: Data from the 6-Month Analysis of the Phase 3 ILLUMINATE-C Trial Background

Primary hyperoxaluria type 1 (PH1) is a rare genetic disorder characterised by hepatic oxalate overproduction that leads to progressive kidney disease. As kidney function declines, oxalate elimination is compromised and plasma oxalate (POx) increases, leading to systemic oxalosis. In chronic kidney disease (CKD) stages 3b-5, elevated POx is directly related to the pathophysiology of oxalosis, and reduction of POx is a relevant clinical trial endpoint. Lumasiran, an RNA interference therapeutic designed to reduce hepatic oxalate production, is indicated for the treatment of PH1 in all age groups. Data from the ILLUMINATE-C trial (EudraCT: 2019-0013346-17) demonstrated substantial reductions in POx and acceptable safety in patients with PH1 with impaired kidney function, including patients on haemodialysis (HD), who received lumasiran for 6 months. In Cohorts A (no HD) and B (on HD), respectively, lumasiran led to 33.33% (95% CI: −15.16, 81.82) and 42.43% (95% CI: 34.15, 50.71) least-squares (LS) mean reductions in POx from baseline to Month 6 (the primary endpoint). Here, additional results from the 6-month primary analysis period of ILLUMINATE-C are presented.

Methods

ILLUMINATE-C is an ongoing Phase 3, single-arm study with two cohorts, Cohort A (N=6; no HD at study start) and Cohort B (N=15; on HD). The 6-month primary analysis period is followed by an extension period (EP) of up to 54 months. Key inclusion criteria include genetically confirmed PH1, eGFR ≤45 mL/min/1.73 m², and POx ≥20 μmol/L. Patients received weight-based dosing of subcutaneous lumasiran. Outcomes included assessments of cardiac systemic oxalosis using echocardiography, medullary nephrocalcinosis by kidney ultrasound, kidney stone events, and burdensome symptoms of PH1.

Results

All 21 patients (43% female; 76% white; median age 8 [range, 0-59] years) completed the 6-month primary analysis period. For Cohort A patients, the median plasma oxalate level was 57.94 μmol/L and the median 24 hour urinary oxalate excretion corrected for body surface area (BSA) at baseline was 2.01 mmol/24 hr/1.73 m2. For Cohort B patients, the median plasma oxalate level was 103.65 μmol/L.

Patients in both cohorts had a reduction in plasma oxalate as early as month 1. The percent change from baseline to Month 6 (average from Month 3 to Month 6) in plasma oxalate levels for Cohort A was an least squares (LS) mean difference of −33.3% (95%).

Among patients with abnormal left ventricular ejection fraction (LVEF; abnormal defined as LVEF <55%) at baseline, 1/1 patient in Cohort A and 2/4 patients in Cohort B showed ≥5% improvement at Month 6. Among patients with abnormal global longitudinal strain (GLS, a measure of LV contractility more sensitive than LVEF for predicting outcomes; abnormal defined as GLS <15%) at baseline, 1/1 patient in Cohort A and 3/3 patients in Cohort B showed ≥2% improvement at Month 6. In Cohort A, 5/6 patients had nephrocalcinosis at baseline; 2 remained stable, none worsened, and 3 improved (2 unilateral and 1 bilateral improvement) at Month 6. In Cohort A, 1 patient did not have nephrocalcinosis at baseline and had bilateral worsening at Month 6. In Cohort B, 2/11 patients had nephrocalcinosis at baseline; both improved (1 unilateral and 1 bilateral improvement). In Cohort A, the rate of kidney stone events per person-year was 3.20 (95% CI: 1.96, 5.22) in the 12 months prior to consent and 1.48 (95% CI: 0.55, 3.92) during the first 6 months of lumasiran treatment. Patients in Cohort B were not expected to have kidney stone events. For patients in both cohorts, the most burdensome symptoms at baseline, including fatigue, nausea/decreased appetite, bone pain, and decreased mobility, improved or remained stable at Month 6; none of the symptoms worsened.

CONCLUSIONS

Lumasiran treatment resulted in substantial reductions in POx in patients of all ages with PH1 and advanced kidney disease. The observations regarding cardiac measures of systemic oxalosis, together with the kidney stone event and nephrocalcinosis results, are consistent with mobilisation of oxalate from systemic stores. Data on these long-term outcomes will continue to be collected and further evaluated in the EP. These results, along with previous reports from ILLUMINATE-A and ILLUMINATE-B, evidence the effectiveness of lumasiran across the full spectrum of disease severity in PH1. 

1.-19. (canceled)
 20. A method for treating a human subject having primary hyperoxaluria type I (PH1), the method comprising administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein treating the subject comprises reducing plasma oxalate levels in the subject, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand differs by no more than 3 bases from the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand differs by no more than 3 bases from the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3′ (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage; and (a) wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, and wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month beginning one month after a last dose of the loading dose; or (b) wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, and wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months beginning one month after a last dose of the loading dose, or (c) wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, and wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months beginning one month after a last dose of the loading dose, thereby treating the human subject having PH1. 21-22. (canceled)
 23. The method of claim 20, wherein the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month beginning one month after a last dose of the loading phase. 24-26. (canceled)
 27. The method of claim 20, wherein the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months beginning one month after a last dose of the loading phase. 28-30. (canceled)
 31. The method of claim 20, wherein the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months beginning one month after a last dose of the loading phase. 32.-38. (canceled)
 39. A method for reducing plasma oxalate in a human subject having primary hyperoxaluria type I (PH1), the method comprising administering to the subject a double stranded RNAi agent that inhibits expression of HAO1, or salt thereof, wherein the double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, wherein the sense strand differs by no more than 3 bases from the nucleotide sequence 5′-gsascuuuCfaUfCfCfuggaaauaua-3′ (SEQ ID NO:14) and the antisense strand differs by no more than 3 bases from the nucleotide sequence 5′-usAfsuauUfuCfCfaggaUfgAfaagucscsa-3′ (SEQ ID NO:15), wherein a, g, c, and u are 2′-O-methyl (2′-OMe) A, G, C, and U, respectively; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C, and U, respectively; and s is a phosphorothioate linkage, and (a) wherein the subject has a body weight of less than about 10 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, and wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month beginning one month after a last dose of the loading phase; or (b) wherein the subject has a body weight of about 10 kg to about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, and wherein the loading phase comprises administering a dose of about 4 milligram per kilogram (mg/kg) to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 4 mg/kg to about 8 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months beginning one month after a last dose of the loading phase; or (c) wherein the subject has a body weight of greater than about 20 kilograms (kg), wherein the double stranded RNAi agent, or salt thereof, is administered in a dosing regimen comprising a loading phase followed by a maintenance phase, and wherein the loading phase comprises administering a dose of about 1 milligram per kilogram (mg/kg) to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months, and the maintenance phase comprises administering a dose of about 1 mg/kg to about 5 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months beginning one month after a last dose of the loading phase, thereby reducing plasma oxalate in the human subject having PH1. 40-41. (canceled)
 42. The method of claim 39, wherein the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month beginning one month after a last dose of the loading phase. 43-45. (canceled)
 46. The method of claim 39, wherein the loading phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and the maintenance phase comprises administering a dose of about 6 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months beginning one month after a last dose of the loading phase. 47-49. (canceled)
 50. The method of claim 39, wherein the loading phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once a month for about three months and the maintenance phase comprises administering a dose of about 3 mg/kg of the double stranded RNAi agent, or salt thereof, to the subject about once every three months beginning one month after a last dose of the loading phase.
 51. The method of claim 39, wherein the plasma oxalate level is reduced by about 35% or more following administration of the double stranded RNAi agent.
 52. The method of claim 39, wherein the plasma oxalate level is reduced to within normal range following administration of the double stranded RNAi agent. 53.-85. (canceled)
 86. The method of claim 20, wherein the RNAi agent, or salt thereof, is administered in a pharmaceutical composition.
 87. The method of claim 20, wherein the double stranded RNAi agent is in a salt form.
 88. The method of claim 20, further comprising administering an additional therapeutic agent to the subject.
 89. (canceled)
 90. The method of claim 20, wherein the subject has end stage renal disease (ESRD) prior to administration of the double stranded RNAi agent; or wherein the subject does not have end stage renal disease (ESRD) prior to administration of the double stranded RNAi agent.
 91. (canceled)
 92. The method of claim 20, wherein the subject is on dialysis; or wherein the subject is not on dialysis.
 93. The method of claim 20, wherein the subject is on dialysis and wherein the double stranded RNAi agent is administered to the subject after dialysis.
 94. The method of claim 20, wherein the double stranded RNAi agent is administered to the subject subcutaneously. 95.-117. (canceled)
 118. The method of claim 20, wherein the double stranded RNAi agent further comprises a ligand attached at the 3′-terminus of the sense strand.
 119. The method of claim 20, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.
 120. The method of claim 118, wherein the ligand is


121. The method of claim 120, wherein the double stranded RNAi agent is conjugated to the ligand as shown in the following schematic

wherein X is O or S. 122.-130. (canceled) 